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Search Results (707)

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Keywords = plant-microbe interaction

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27 pages, 1218 KiB  
Review
Non-Rhizobial Endophytes (NREs) of the Nodule Microbiome Have Synergistic Roles in Beneficial Tripartite Plant–Microbe Interactions
by Ahmed Idris Hassen, Esther K. Muema, Mamonokane O. Diale, Tiisetso Mpai and Francina L. Bopape
Microorganisms 2025, 13(3), 518; https://doi.org/10.3390/microorganisms13030518 - 26 Feb 2025
Viewed by 1
Abstract
Abstract: Microbial symbioses deal with the symbiotic interactions between a given microorganism and another host. The most widely known and investigated microbial symbiosis is the association between leguminous plants and nitrogen-fixing rhizobia. It is one of the best-studied plant–microbe interactions that occur [...] Read more.
Abstract: Microbial symbioses deal with the symbiotic interactions between a given microorganism and another host. The most widely known and investigated microbial symbiosis is the association between leguminous plants and nitrogen-fixing rhizobia. It is one of the best-studied plant–microbe interactions that occur in the soil rhizosphere and one of the oldest plant–microbe interactions extensively studied for the past several decades globally. Until recently, it used to be a common understanding among scientists in the field of rhizobia and microbial ecology that the root nodules of thousands of leguminous species only contain nitrogen-fixing symbiotic rhizobia. With the advancement of molecular microbiology and the coming into being of state-of-the-art biotechnology innovations, including next-generation sequencing, it has now been revealed that rhizobia living in the root nodules of legumes are not alone. Microbiome studies such as metagenomics of the root nodule microbial community showed that, in addition to symbiotic rhizobia, other bacteria referred to as non-rhizobial endophytes (NREs) exist in the nodules. This review provides an insight into the occurrence of non-rhizobial endophytes in the root nodules of several legume species and the beneficial roles of the tripartite interactions between the legumes, the rhizobia and the non-rhizobial endophytes (NREs). Full article
(This article belongs to the Section Plant Microbe Interactions)
26 pages, 17005 KiB  
Article
Unraveling the Mechanism of the Endophytic Bacterial Strain Pseudomonas oryzihabitans GDW1 in Enhancing Tomato Plant Growth Through Modulation of the Host Transcriptome and Bacteriome
by Waqar Ahmed, Yan Wang, Wenxia Ji, Songsong Liu, Shun Zhou, Jidong Pan, Zhiguang Li, Fusheng Wang and Xinrong Wang
Int. J. Mol. Sci. 2025, 26(5), 1922; https://doi.org/10.3390/ijms26051922 - 23 Feb 2025
Viewed by 213
Abstract
Endophytic Pseudomonas species from agricultural crops have been extensively studied for their plant-growth-promoting (PGP) potential, but little is known about their PGP potential when isolated from perennial trees. This study investigated the plant-growth-promoting (PGP) potential of an endophyte, Pseudomonas oryzihabitans GDW1, isolated from [...] Read more.
Endophytic Pseudomonas species from agricultural crops have been extensively studied for their plant-growth-promoting (PGP) potential, but little is known about their PGP potential when isolated from perennial trees. This study investigated the plant-growth-promoting (PGP) potential of an endophyte, Pseudomonas oryzihabitans GDW1, isolated from a healthy pine tree by taking tomato as a host plant. We employed multiomics approaches (transcriptome and bacteriome analyses) to elucidate the underlying PGP mechanisms of GDW1. The results of greenhouse experiments revealed that the application of GDW1 significantly improved tomato plant growth, increasing shoot length, root length, fresh weight, and biomass accumulation by up to 44%, 38%, 54%, and 59%, respectively, compared with control. Transcriptomic analysis revealed 1158 differentially expressed genes significantly enriched in the plant hormone signaling (auxin, gibberellin, and cytokinin) and stress response (plant–pathogen interaction, MAPK signaling pathway-plant, and phenylpropanoid biosynthesis) pathways. Protein–protein interaction network analysis revealed nine hub genes (MAPK10, ARF19-1, SlCKX1, GA2ox2, PAL5, SlWRKY37, GH3.6, XTH3, and NML1) related to stress tolerance, hormone control, and plant defense. Analysis of the tomato root bacteriome through 16S rRNA gene amplicon sequencing revealed that GDW1 inoculation dramatically altered the root bacterial community structure, enhancing the diversity and abundance of beneficial taxa (Proteobacteria and Bacteroidota). Co-occurrence network analysis showed a complex bacterial network in treated plants, suggesting increasingly intricate microbial relationships and improved nutrient absorption. Additionally, FAPROTAX and PICRUSt2 functional prediction analyses suggested the role of GDW1 in nitrogen cycling, organic matter degradation, plant growth promotion, and stress resistance. In conclusion, this study provides novel insights into the symbiotic relationship between P. oryzihabitans GDW1 and tomato plants, highlighting its potential as a biofertilizer for sustainable agriculture and a means of reducing the reliance on agrochemicals. Full article
(This article belongs to the Special Issue The Molecular Basis of Plant–Microbe Interactions)
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16 pages, 2758 KiB  
Article
De Novo Leaf Transcriptome Assembly and Metagenomic Studies of Coast Live Oak (Quercus agrifolia)
by Savanah Senn, Ray A. Enke, Steven J. Carrell, Bradley Nations, Meika Best, Mathew Kostoglou, Karu Smith, Jieyao Yan, Jillian M. Ford, Les Vion and Gerald Presley
Appl. Microbiol. 2025, 5(1), 24; https://doi.org/10.3390/applmicrobiol5010024 - 22 Feb 2025
Viewed by 235
Abstract
Coast Live Oak (Quercus agrifolia) is a native keystone hardwood species of the California coastal and semi-arid forest environment. Q. agrifolia is threatened by pathogens such as the oomycete Phytophthora ramorum, which is known to cause Sudden Oak Death in [...] Read more.
Coast Live Oak (Quercus agrifolia) is a native keystone hardwood species of the California coastal and semi-arid forest environment. Q. agrifolia is threatened by pathogens such as the oomycete Phytophthora ramorum, which is known to cause Sudden Oak Death in environments from Southern California to Oregon. This study considers oaks and their rootzone microbes recovering from moderate and low-intensity fires in rapid succession, compared to high- and low-intensity fires with a large time gap between them. cDNA libraries from nine oak leaf tissue samples were sequenced on DNBseq. Soil samples were sent out for shotgun metagenomics and for 16S community profiling. The de novo Q. agrifolia assembly yielded 521,817 transcripts with an average length of 805.2 bp. Among identified DEGs (differentially expressed genes) between the trail areas, several candidate genes were identified including shikimate dehydrogenase and myrcene synthase. The MegaBLAST results showed a high degree of similarity to WGS sequences from Q. agrifolia that had been previously annotated in other closely related Quercus species. There was a differential abundance of microbial genera associated with the different burn areas, including Pedobacter, Filimonas, Cohnella, and Sorangium. The data embody the first Q. agrifolia transcriptome that with further development could be used to screen oak seedlings for resistance; beneficial microbial populations have been identified that are associated with fire recovery under varied conditions. Full article
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21 pages, 976 KiB  
Review
Engineering Synthetic Microbial Communities: Diversity and Applications in Soil for Plant Resilience
by Arneeb Tariq, Shengzhi Guo, Fozia Farhat and Xihui Shen
Agronomy 2025, 15(3), 513; https://doi.org/10.3390/agronomy15030513 - 20 Feb 2025
Viewed by 153
Abstract
Plants host a complex but taxonomically assembled set of microbes in their natural environment which confer several benefits to the host plant including stress resilience, nutrient acquisition and increased productivity. To understand and simplify the intricate interactions among these microbes, an innovative approach—Synthetic [...] Read more.
Plants host a complex but taxonomically assembled set of microbes in their natural environment which confer several benefits to the host plant including stress resilience, nutrient acquisition and increased productivity. To understand and simplify the intricate interactions among these microbes, an innovative approach—Synthetic Microbial Community (SynCom)—is practiced, involving the intentional co-culturing of multiple microbial taxa under well-defined conditions mimicking natural microbiomes. SynComs hold promising solutions to the issues confronted by modern agriculture stemming from climate change, limited resources and land degradation. This review explores the potential of SynComs to enhance plant growth, development and disease resistance in agricultural settings. Despite the promising potential, the effectiveness of beneficial microbes in field applications has been inconsistent. Computational simulations, high-throughput sequencing and the utilization of omics databases can bridge the information gap, providing insights into the complex ecological and metabolic networks that govern plant–microbe interactions. Artificial intelligence-driven models can predict complex microbial interactions, while machine learning algorithms can analyze vast datasets to identify key microbial taxa and their functions. We also discuss the barriers to the implementation of these technologies in SynCom engineering. Future research should focus on these innovative applications to refine SynCom strategies, ultimately contributing to the advancement of green technologies in agriculture. Full article
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14 pages, 950 KiB  
Review
Biological Guardians: Unveiling Microbial Solutions to Combat Cannabis sativa Fungal Pathogens
by S. M. Ahsan, Md. Injamum-Ul-Hoque, Ashim Kumar Das, Muhammad Imran, Soosan Tavakoli, Da Bin Kwon, Sang-Mo Kang, In-Jung Lee and Hyong Woo Choi
Stresses 2025, 5(1), 16; https://doi.org/10.3390/stresses5010016 - 17 Feb 2025
Viewed by 262
Abstract
Cannabis (Cannabis sativa L.) is one of the earliest cultivated crops and is valued for its medicinal compounds, food, fibre, and bioactive secondary metabolites. The rapid expansion of the cannabis industry has surpassed the development of production system knowledge. The scientific community [...] Read more.
Cannabis (Cannabis sativa L.) is one of the earliest cultivated crops and is valued for its medicinal compounds, food, fibre, and bioactive secondary metabolites. The rapid expansion of the cannabis industry has surpassed the development of production system knowledge. The scientific community currently focuses on optimising agronomic and environmental factors to enhance cannabis yield and quality. However, cultivators face significant challenges from severe pathogens, with limited effective control options. The principal diseases include root rot, wilt, bud rot, powdery mildew, cannabis stunt disease, and microorganisms that reduce post-harvest quality. Sustainable management strategies involve utilising clean planting stocks, modifying environmental conditions, implementing sanitation, applying fungal and bacterial biological control agents, and drawing on decades of research on other crops. Plant–microbe interactions can promote growth and regulate secondary metabolite production. This review examines the recent literature on pathogen management in indoor cannabis production using biocontrol agents. Specific morphological, biochemical, and agronomic characteristics hinder the implementation of biological control strategies for cannabis. Subsequent investigations should focus on elucidating the plant–microbe interactions essential for optimising the effectiveness of biological control methodologies in cannabis cultivation systems. Full article
(This article belongs to the Collection Feature Papers in Plant and Photoautotrophic Stresses)
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19 pages, 811 KiB  
Review
Uncovering the Host Range–Lifestyle Relationship in the Endophytic and Anthracnose Pathogenic Genus Colletotrichum
by Jacy Newfeld, Ren Ujimatsu and Kei Hiruma
Microorganisms 2025, 13(2), 428; https://doi.org/10.3390/microorganisms13020428 - 16 Feb 2025
Viewed by 279
Abstract
Colletotrichum includes agriculturally and scientifically important pathogens that infect numerous plants. They can also adopt an endophytic lifestyle, refraining from causing disease and/or even promoting plant growth when inoculated on a non-susceptible host. In this manner, the host range of a Colletotrichum fungus [...] Read more.
Colletotrichum includes agriculturally and scientifically important pathogens that infect numerous plants. They can also adopt an endophytic lifestyle, refraining from causing disease and/or even promoting plant growth when inoculated on a non-susceptible host. In this manner, the host range of a Colletotrichum fungus can shift, depending on whether it exhibits endophytic or pathogenic lifestyles. Some fungi, such as Colletotrichum tofieldiae, can even shift between pathogenicity and endophytism within the same host depending on the environmental conditions. Here, we aim to disentangle the relationship between lifestyle and host range in Colletotrichum. Specifically, we aim to demonstrate that lifestyle is dependent on the host colonized in many Colletotrichum fungi. We discuss the ways in which pathogenic Colletotrichum species may act endophytically on alternative hosts, how comparative genomics has uncovered candidate molecules (namely effectors, CAZymes, and secondary metabolites) underlying fungal lifestyle, and the merits of using endophytic fungi alongside pathogenic fungi in research, which facilitates the use of reverse genetics to uncover molecular determinants of lifestyle. In particular, we reference the Arabidopsis thalianaColletotrichum tofieldiae study system as a model for elucidating the dual roles of plant–fungus interactions, both endophytic and pathogenic, through integrative omics approaches and reverse genetics. This is because C. tofieldiae contains closely related pathogens and endophytes, making it an ideal model for identifying candidate determinants of lifestyle. This approach could identify key molecular targets for effective pathogen management in agriculture. Lastly, we propose a model in which pathogenic lifestyle occupies a different host range than the endophytic lifestyle. This will enhance our understanding of pathogenicity and endophytism in a globally significant fungal genus and lay the groundwork for future research examining molecular determinants of lifestyle in plant-associated fungi. Full article
(This article belongs to the Special Issue Colletotrichum Pathogens in Plants)
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27 pages, 1050 KiB  
Review
A Review of Biochar from Biomass and Its Interaction with Microbes: Enhancing Soil Quality and Crop Yield in Brassica Cultivation
by Kritsana Jatuwong, Worawoot Aiduang, Tanongkiat Kiatsiriroat, Wassana Kamopas and Saisamorn Lumyong
Life 2025, 15(2), 284; https://doi.org/10.3390/life15020284 - 12 Feb 2025
Viewed by 505
Abstract
Biochar, produced from biomass, has become recognized as a sustainable soil amendment that has the potential to improve soil quality and agricultural production. This review focuses on production processes and properties of biochar derived from different types of biomass, including the synergistic interactions [...] Read more.
Biochar, produced from biomass, has become recognized as a sustainable soil amendment that has the potential to improve soil quality and agricultural production. This review focuses on production processes and properties of biochar derived from different types of biomass, including the synergistic interactions between biochar and soil microorganisms, emphasizing their influence on overall soil quality and crop production, particularly in cultivation of Brassica crops. It additionally addresses the potential benefits and limitations of biochar and microbial application. Biomass is a renewable and abundant resource and can be converted through pyrolysis into biochar, which has high porosity, abundant surface functionalities, and the capacity to retain nutrients. These characteristics provide optimal conditions for beneficial microbial communities that increase nutrient cycling, reduce pathogens, and improve soil structure. The information indicates that the use of biochar in Brassica crops can result in improved plant growth, yield, nutrient uptake, and stress mitigation. This review includes information about biochar properties such as pH, elemental composition, ash content, and yield, which can be affected by the different types of biomass used as well as pyrolysis conditions like temperature. Understanding these variables is essential for optimizing biochar for agricultural use. Moreover, the information on the limitations of biochar and microbes emphasizes the importance of their benefits with potential constraints. Therefore, sustainable agriculture methods can possibly be achieved by integrating biochar with microbial management measurements, resulting in higher productivity and adaptability in Brassica or other plant crop cultivation systems. This review aims to provide a comprehensive understanding of biochar’s role in supporting sustainable Brassica farming and its potential to address contemporary agricultural challenges. Full article
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20 pages, 3408 KiB  
Article
Microbial Allies or Adversaries? The Genotype-Dependent Impact of Inoculation on Silver Birch
by Greta Striganavičiūtė, Dorotėja Vaitiekūnaitė, Milana Šilanskienė and Vaida Sirgedaitė-Šėžienė
Plants 2025, 14(4), 545; https://doi.org/10.3390/plants14040545 - 10 Feb 2025
Viewed by 365
Abstract
Microbial inoculation plays a crucial role in shaping plant physiological and biochemical responses, influencing growth, secondary metabolism, and stress-related markers. This study investigates the effects of PAH-degrading microorganisms (Pseudomonas putida, Sphingobium yanoikuyae, and Rhodotorula sphaerocarpa) on the growth, secondary metabolism, [...] Read more.
Microbial inoculation plays a crucial role in shaping plant physiological and biochemical responses, influencing growth, secondary metabolism, and stress-related markers. This study investigates the effects of PAH-degrading microorganisms (Pseudomonas putida, Sphingobium yanoikuyae, and Rhodotorula sphaerocarpa) on the growth, secondary metabolism, photosynthetic pigment, and stress-related biochemical markers of silver birch (Betula pendula Roth) seedlings from two half-sib families grown hydroponically. Results demonstrate family-dependent variations in the response to microbial treatments. In family 73, the growth of both shoots and roots was inhibited by certain microbial treatments, along with a decrease in key biochemical markers such as phenolic content and carotenoids. Conversely, family 86 showed no growth inhibition and exhibited improvements in some biochemical markers, including flavonoids and chlorophyll. Stress indicators, such as malondialdehyde (MDA) and soluble sugars, displayed contrasting patterns between families, with increased MDA observed in family 73 under certain microbial treatments. In contrast, family 86 did not exhibit an increase in MDA, suggesting differences in stress mitigation. Soluble sugars were generally reduced in family 73. Antioxidant enzyme activity further highlighted these family-specific responses, with variations in enzymes like ascorbate peroxidase (APX) and guaiacol peroxidase (POX) across treatments. Notably, significant interactions between family and microbial treatments were observed for several oxidative stress enzymes, underscoring the role of genotype in shaping the response to microbial stress. These findings highlight the genotype-dependent interactions between microbial inoculation and plant secondary metabolism, providing insights into the role of specifically selected microbial inoculation in stress mitigation and growth regulation. Full article
(This article belongs to the Section Plant Protection and Biotic Interactions)
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21 pages, 28679 KiB  
Article
Transgenic Maize of ZmMYB3R Shapes Microbiome on Adaxial and Abaxial Surface of Leaves to Promote Disease Resistance
by Shengqian Chao, Yin Zhang, Yue Hu, Yifan Chen, Peng Li, Yu Sun, Lili Song, Yingxiong Hu, Hui Wang, Jiandong Wu and Beibei Lv
Microorganisms 2025, 13(2), 362; https://doi.org/10.3390/microorganisms13020362 - 7 Feb 2025
Viewed by 452
Abstract
The phyllosphere is one of the largest habitats for microorganisms, and host genetic factors play an important role during the interaction between microorganisms and the phyllosphere. Therefore, the transgene may also lead to changes in the maize phyllosphere. ZmMYB3R was identified as a [...] Read more.
The phyllosphere is one of the largest habitats for microorganisms, and host genetic factors play an important role during the interaction between microorganisms and the phyllosphere. Therefore, the transgene may also lead to changes in the maize phyllosphere. ZmMYB3R was identified as a drought-tolerant gene in Arabisopsis. Here, we employed metagenomic sequencing to analyze the microbiome of the adaxial and abaxial leaf surfaces on ZmMYB3R-overexpressing (OE) and wild-type (WT)·maize, aiming to dissect the possible associations between ZmMYB3R and changes in phyllosphere microbiome functioning. Our results revealed that overexpressing ZmMYB3R altered the alpha and beta diversity of the phyllosphere microbiome. In OE plants, more beneficial microbes accumulated on the phyllosphere, while pathogenic ones diminished, especially on the abaxial surface of ZmMYB3R leaves. Further analysis of disease resistance-related metabolic pathways and abundances of disease resistance genes revealed significant differences between OE and WT. The inoculation experiment between OE and WT proved that ZmMYB3R increased the disease resistance of maize. In conclusion, the results reveal that transgenes affect the phyllosphere microbiome, and ZmMYB3R might alter leaf disease resistance by reshaping the phyllosphere microbiome structure. These findings help us understand how ZmMYB3R regulates leaf disease resistance and may facilitate the development of disease control by harnessing beneficial microbial communities. Full article
(This article belongs to the Special Issue Beneficial Microbes: Food, Mood and Beyond, 2nd Edition)
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21 pages, 3439 KiB  
Article
Labile Carbon Input Mitigates the Negative Legacy Effects of Nitrogen Addition on Arbuscular Mycorrhizal Symbiosis in a Temperate Grassland
by Sitong Liu, Yuxiao Zhang, Xiaoqian Yu, Meng Cui, Liangchao Jiang, Tao Zhang and Yingzhi Gao
Plants 2025, 14(3), 456; https://doi.org/10.3390/plants14030456 - 4 Feb 2025
Viewed by 418
Abstract
Nitrogen (N) deposition and carbon (C) addition significantly influence the dynamics of plant–microbe interactions, particularly altering the symbiotic relationship between plants and arbuscular mycorrhizal fungi (AMF). However, the effects and underlying mechanisms of labile C input on the relationship between AMF and various [...] Read more.
Nitrogen (N) deposition and carbon (C) addition significantly influence the dynamics of plant–microbe interactions, particularly altering the symbiotic relationship between plants and arbuscular mycorrhizal fungi (AMF). However, the effects and underlying mechanisms of labile C input on the relationship between AMF and various plant species in a nitrogen-enriched environment remain a knowledge gap. A seven-year field experiment was conducted to examine how six levels of N and three levels of labile C addition impact AMF colonization in four key plant species: Leymus chinensis (Trin. ex Bunge) Tzvelev, Stipa baicalensis Roshev., Thermopsis lanceolata R. Br. and Potentilla bifurca Linn. Our results showed that N and C additions exert significantly different effects on the relationship between AMF and various plant species. Labile C addition mitigated historical N negative effects, particularly for S. baicalensis, enhancing AMF infection and promoting nutrient exchange under high-N and low-C conditions. The relationship between AMF and both L. chinensis and T. lanceolata changed to weak mutualism under low-N and high-C conditions, with significant decreases in vesicular and arbuscular abundance. Plant root stoichiometry plays a critical role in modulating AMF symbiosis, particularly under high-N and -C conditions, as reflected in the increased AMF infection observed in T. lanceolata and P. bifurca. Our findings emphasize the species-specific and nutrient-dependent AMF symbiosis, revealing that targeted C input can mitigate the legacy effects of N enrichment. Effective nutrient management is of crucial importance for ecological restoration efforts in temperate grasslands affected by long-term N enrichment. Full article
(This article belongs to the Special Issue Plant-Soil Microbe Interactions in Ecosystems)
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18 pages, 4474 KiB  
Article
Salt Tolerance Induced by Plant Growth-Promoting Rhizobacteria Is Associated with Modulations of the Photosynthetic Characteristics, Antioxidant System, and Rhizosphere Microbial Diversity in Soybean (Glycine max (L.) Merr.)
by Tong Lin, Fasih Ullah Haider, Tianhao Liu, Shuxin Li, Peng Zhang, Chunsheng Zhao and Xiangnan Li
Agronomy 2025, 15(2), 341; https://doi.org/10.3390/agronomy15020341 - 28 Jan 2025
Viewed by 653
Abstract
Salinity stress poses a major obstacle to agricultural productivity. Employing plant growth-promoting rhizobacteria (PGPR) has attracted significant attention due to its potential to improve plant development in challenging conditions. Yet, additional investigation is essential to fully understand the potential of PGPR in mitigating [...] Read more.
Salinity stress poses a major obstacle to agricultural productivity. Employing plant growth-promoting rhizobacteria (PGPR) has attracted significant attention due to its potential to improve plant development in challenging conditions. Yet, additional investigation is essential to fully understand the potential of PGPR in mitigating salinity stress, especially in field applications. Hence, this study investigated the resistance mechanisms of soybean (Glycine max (L.) Merr.) under salt stress with PGPR application through a field experiment with four treatments: normal soybean planting (NN), normal planting + PGPR (NP), salt stress planting (SN), and salt stress planting + PGPR (SP). This research investigated how applying PGPR under salt stress influences soybean photosynthetic traits, osmotic regulation, rhizosphere microbial communities, and yield quality. The results demonstrated that salt stress enhanced leaf temperature and significantly reduced the leaf area index, SPAD value, stomatal conductance, photosynthetic rate, and transpiration rate of soybeans. Compared to SN treatment, SP treatment significantly improved the stomatal conductance, photosynthetic rate, and transpiration rate by 10.98%, 16.28%, and 35.59%, respectively. Salt stress substantially increased sodium (Na+) concentration and Na+/K+ ratio in leaves, roots, and grains while reducing potassium (K+) concentration in roots and leaves. Under salinity stress, PGPR application significantly minimized Na+ concentration in leaves and enhanced K⁺ concentration in leaves, roots, and grains by 47.05%, 25.72%, and 14.48%, respectively. PGPR application boosted carbon assimilation (starch synthesis) by enhancing the activities of sucrose synthase, fructokinase, and ADP-glucose pyrophosphorylase. It improved physiological parameters and increased soybean yield by 32.57% compared to SN treatment. Additionally, PGPR enhanced antioxidant enzyme activities, including glutathione reductase, peroxidase, ascorbate peroxidase, and monodehydroascorbate reductase, reducing oxidative damage from salt stress. Analysis of rhizosphere microbial communities revealed that PGPR application enriched beneficial bacterial phyla such as Bacteroidetes, Firmicutes, Nitrospirae, and Patescibacteria and fungal genera like Metarhizium. These microbial shifts likely contributed to improved nutrient cycling and plant–microbe interactions, further enhancing soybean resilience to salinity. This study demonstrates that PGPR enhances soybean growth, microbial diversity, and salt tolerance under salinity stress, while future efforts should optimize formulations, explore synergies, and scale up for sustainable productivity. Full article
(This article belongs to the Section Crop Breeding and Genetics)
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15 pages, 2834 KiB  
Article
Populations of Heterodera schachtii Differ in Susceptibility to Rhizosphere Bacteria Structured by Plant Age
by Rasha Haj Nuaima, Eva Tanneau and Holger Heuer
Microorganisms 2025, 13(2), 289; https://doi.org/10.3390/microorganisms13020289 - 28 Jan 2025
Viewed by 535
Abstract
Rhizosphere microbes, particularly bacteria, are essential for controlling plant-parasitic nematodes (PPNs) through various mechanisms. However, the plant’s age and the genetic composition of nematode populations can significantly influence the inhibitory effectiveness of these microbes against the beet cyst nematode Heterodera schachtii. In [...] Read more.
Rhizosphere microbes, particularly bacteria, are essential for controlling plant-parasitic nematodes (PPNs) through various mechanisms. However, the plant’s age and the genetic composition of nematode populations can significantly influence the inhibitory effectiveness of these microbes against the beet cyst nematode Heterodera schachtii. In this study, rhizosphere microbes were isolated from 39-day-old and 69-day-old resistant oilseed radish plants to evaluate their impact on the penetration of the second-stage juveniles (J2s) originating from four genetically distinct H. schachtii populations. The suppression of J2s penetration by the attached microbes varied across the nematode populations, which displayed differing levels of aggressiveness toward the resistant oilseed radish. Furthermore, differences in the alpha and beta diversity of rhizosphere bacteria were observed between the 39-day-old and 69-day-old plants, leading to variations in the bacterial attachment among the four nematode populations. In summary, the effectiveness of resistant catch crops against H. schachtii is influenced by the pathogenicity of the nematode populations and their interactions with the rhizosphere microbial community shaped by the plant’s age. Full article
(This article belongs to the Section Plant Microbe Interactions)
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17 pages, 1053 KiB  
Review
From Recognition to Response: Resistance–Effector Gene Interactions in the Brassica napus and Leptosphaeria maculans Patho-System
by Zuhra Qayyum, William J. W. Thomas, Junrey C. Amas, Maria Pazos-Navarro and Jacqueline Batley
Plants 2025, 14(3), 390; https://doi.org/10.3390/plants14030390 - 27 Jan 2025
Viewed by 718
Abstract
Blackleg disease, caused by the hemibiotrophic fungal pathogen Leptosphaeria maculans, poses a serious threat to Brassica crops and requires a broad understanding of the plant defence mechanisms. The Brassica. napus-L. maculans pathosystem provides a useful model to understand plant resistance [...] Read more.
Blackleg disease, caused by the hemibiotrophic fungal pathogen Leptosphaeria maculans, poses a serious threat to Brassica crops and requires a broad understanding of the plant defence mechanisms. The Brassica. napus-L. maculans pathosystem provides a useful model to understand plant resistance response to hemibiotrophs. This review aims to explain the mechanisms underlying R-Avr interaction, signalling cascades, and the hypersensitive response (HR) produced by B. napus towards L. maculans, causing local cell death that restricts the pathogen to the site of infection. The role of transcription factors is pivotal to the process of HR, coordinating the regulation of genes involved in pathogen recognition and the activation of SA responsive genes and production of secondary metabolites. The R-Avr interaction signalling cascade involves production of reactive oxygen species (ROS), calcium ion influx, Salicylic acid (SA) hormonal signalling and mitogen activated protein kinases (MAPKs), which are critical in the HR in B. napus. The in-depth understanding of molecular signalling pathway of the R-Avr interaction between B. napus-L. maculans pathosystem provides valuable information for future research endeavours regarding enhancing disease resistance in Brassica crops. Full article
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16 pages, 5107 KiB  
Article
The Identification of a Unique Gene MoUNG Required for Growth, Conidiation, and Pathogenicity in Magnaporthe oryzae Through T-DNA Insertion Mutagenesis
by Jing Chen, Qingfeng He, Xuze Xie, Yuting Wu, Shan Liu, Xihong Li, Xianfeng Yi, Dan Zhang, Stefan Olsson, Guodong Lu, Zonghua Wang, Youjian Zhang, Meizhen Lin and Ya Li
Agronomy 2025, 15(2), 298; https://doi.org/10.3390/agronomy15020298 - 25 Jan 2025
Viewed by 428
Abstract
Unique genes refer to genes specific to a particular organism and play crucial roles in the biological functions, evolutionary processes, and adaptations to external environments. However, the roles of unique genes in plant pathogenic fungi remain largely unexplored. In this study, we identified [...] Read more.
Unique genes refer to genes specific to a particular organism and play crucial roles in the biological functions, evolutionary processes, and adaptations to external environments. However, the roles of unique genes in plant pathogenic fungi remain largely unexplored. In this study, we identified a novel unique gene in the rice blast fungus Magnaporthe oryzae, named MoUNG (M. oryzae unique gene), through T-DNA insertion mutagenesis. The disruption of the MoUNG promoter region in the T-DNA insertion mutant (T30-104) led to an almost loss of MoUNG expression. MoUNG has no functional domains and lacks homologues in other organism. It is highly expressed during the early-infection stage between 16 and 32 h post-inoculation (HPI), in contrast to its expression in mycelia and at the later infection stage of 48 HPI. Notably, attempts to knock out MoUNG were unsuccessful, so we examined the T30-104 mutant and found it showed significantly reduced growth, conidiation, and pathogenicity. Introducing the full-length MoUNG with its promoter into T30-104 restored these phenotypic defects. Additionally, subcellular localization assays revealed that MoUNG exhibits a dot-like distribution within the cytoplasm of mycelium, conidium, appressorium, and invasive hypha. Furthermore, knock-down of MoUNG produced results similar to those observed with the insertion mutation. In conclusion, we identified a novel unique gene MoUNG in M. oryzae and demonstrated its involvement in growth, conidiation, and pathogenicity. Full article
(This article belongs to the Special Issue The Mechanism of Pathogen Infection and Defense in Crops)
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18 pages, 3308 KiB  
Article
Microbial Communities in Permafrost, Moraine and Deschampsia antarctica Rhizosphere Soils near Ecology Glacier (King George Island, Maritime Antarctic)
by Daniel E. Palma, Alexis Gaete, Dariel López, Andrés E. Marcoleta, Francisco P. Chávez, León A. Bravo, Jacquelinne J. Acuña, Verónica Cambiazo and Milko A. Jorquera
Diversity 2025, 17(2), 86; https://doi.org/10.3390/d17020086 - 25 Jan 2025
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Abstract
While the recession of glaciers in the Antarctic is of global concern under climate change, the impact of deglaciation on soil microbiomes is still limited. Here, soil samples were collected from permafrost (P), moraine (M) and Deschampsia antarctica rhizosphere (R) soils near Ecology [...] Read more.
While the recession of glaciers in the Antarctic is of global concern under climate change, the impact of deglaciation on soil microbiomes is still limited. Here, soil samples were collected from permafrost (P), moraine (M) and Deschampsia antarctica rhizosphere (R) soils near Ecology Glacier (Antarctic), and their soil physicochemical properties and microbial communities (bacteria, archaea and fungi) were characterized. Our analyses showed that there were significant differences in the soil properties and microbial communities between the R samples and the P and M samples. Specifically, amplicon sequencing of 16S rDNA revealed high bacterial richness and diversity in the studied soils, which were dominated mainly by the phyla Proteobacteria, Actinobacteriota and Bacteroidota. In contrast, lower richness and diversity were observed in the archaeal communities, which were dominated by the phyla Chenarchaeota (M and R) and Thermoplasmadota (M). In addition, fungal community analysis revealed a lower richness and diversity (M and R), dominated by the phylum Ascomycota. Our observations are consistent with previous reports describing the relevant changes in soil microbial communities during glacial recession, including fewer microbial groups studied in soils (archaea and fungi). However, further studies are still needed to elucidate the contributions of microbial communities to soil formation and plant colonization in ice-free soils in Antarctica under global climate change. Full article
(This article belongs to the Special Issue 2024 Feature Papers by Diversity’s Editorial Board Members)
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