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15 pages, 1763 KB

Open AccessArticle

Effects of the IAA-Producing Endophytic Bacillus spp. on the Growth of Hordeum vulgare L.

by Murat Güler

Microorganisms 2026, 14(5), 1069; https://doi.org/10.3390/microorganisms14051069 - 9 May 2026

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Abstract

Endophytic bacteria are beneficial microbes that live within plant tissues and promote growth through nitrogen fixation, phosphate solubilization, and phytohormone production. Two endophytic isolates from bell pepper (Capsicum annuum L.) root were identified based on their morphology and biochemical properties using 16S [...] Read more.

Endophytic bacteria are beneficial microbes that live within plant tissues and promote growth through nitrogen fixation, phosphate solubilization, and phytohormone production. Two endophytic isolates from bell pepper (Capsicum annuum L.) root were identified based on their morphology and biochemical properties using 16S rRNA gene sequencing. Winter barley seeds were inoculated with two PGP (plant growth-promoting) bacterial strains (C-14 and C-27), previously characterized for indole-derived compound (IDC) production, and evaluated in a pot experiment with four treatments: Treatment A1 (C-14), Treatment A2 (C-27), Treatment A3 Consortium (C-14 + C-27), and Treatment A4 (non-inoculated control). The results indicated that root and stem lengths increased in plants inoculated with bacteria compared to the uninoculated control. Among treatments, A2 produced the greatest root and shoot lengths (17.23 and 26.2 cm), while A3 showed the lowest (15.8 and 21.5 cm). SPAD values also increased by 6%, 10%, and 3.2% in Treatments A1, A2, and A3, respectively. This study clearly demonstrated that the endophytic isolates (C-14 and C-27) obtained from bell pepper roots significantly enhanced the growth of barley due to their ability of IDC production, thereby offering a promising alternate to chemical fertilizers. Full article

(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

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15 pages, 6196 KB

Open AccessArticle

Plant–Soil–Microbe Interactions Along a Salinity Gradient in the Songnen Plain Grasslands

by Haotian Li, Wenbo Zhu, Tianen Hu, Yilin Chen, Zhihao Han, Huichuan Xiao, Ligang Qin and Linlin Mei

Microorganisms 2026, 14(4), 860; https://doi.org/10.3390/microorganisms14040860 - 11 Apr 2026

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Abstract

The salinization of natural grasslands is a growing global concern. The Songnen Plain in northeastern China represents a typical soda–saline grassland region, yet an integrated understanding of how salinization reshapes plant, soil, and microbial components in this ecosystem remains limited. In this study, [...] Read more.

The salinization of natural grasslands is a growing global concern. The Songnen Plain in northeastern China represents a typical soda–saline grassland region, yet an integrated understanding of how salinization reshapes plant, soil, and microbial components in this ecosystem remains limited. In this study, we investigated plant community characteristics, soil physicochemical properties, and soil microbial communities across a salinity gradient (from non-saline to extremely severe saline) using field surveys, laboratory analyses, and structural equation modeling (SEM). Our results showed that vegetation species diversity, the Shannon–Wiener index, and Simpson’s index all decreased from mild to severe salinization. Soil nutrient indicators, including total nitrogen (TN), total phosphorus (TP), and total potassium (TK), significantly decreased with increasing salinity. SEM revealed that plant community diversity had a significant positive effect on soil microorganisms, whereas soil properties, particularly available potassium (AK) and electrical conductivity (EC), exerted significant negative effects on microbial diversity. Together, these results provide an integrated view of how salinization restructures plant–soil–microbe interactions across the Songnen Plain grasslands. These findings improve understanding of saline–alkali grassland degradation from a plant–soil–microbe perspective and provide a theoretical basis for ecosystem restoration in this region. Full article

(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

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21 pages, 4076 KB

Open AccessArticle

Changes in Soil Microorganisms After Planting Idesia polycarpa in the Luohe River Basin

by Xiaolong Hao, Qifei Cai, Tong Niu, Yingjian Niu, Zhongyu Wang, Zhen Liu, Yanmei Wang, Xiaodong Geng, Juan Wang, Yongyu Ren, Fangming Liu, Yaohui Liu, Li Dai and Zhi Li

Microorganisms 2026, 14(3), 646; https://doi.org/10.3390/microorganisms14030646 - 13 Mar 2026

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Abstract

Idesia polycarpa ‘Yitong 2’ is a high-oil cultivar widely promoted in central China, yet field evidence on how soil bacterial communities respond during early plantation establishment remains limited. Here, we conducted fixed-site monitoring in a newly established ‘Yitong 2’ plantation in the Luohe [...] Read more.

Idesia polycarpa ‘Yitong 2’ is a high-oil cultivar widely promoted in central China, yet field evidence on how soil bacterial communities respond during early plantation establishment remains limited. Here, we conducted fixed-site monitoring in a newly established ‘Yitong 2’ plantation in the Luohe River Basin (Henan, China). Bulk soil (0–30 cm) was collected before planting (March 2024) and at 3, 6 and 12 months after planting (June 2024, September 2024 and March 2025). Soil physicochemical properties were measured and bacterial communities were profiled by 16S rRNA gene (V3–V4) amplicon sequencing; functional potential was inferred using PICRUSt2. Available potassium increased significantly, whereas soil organic matter showed a decrease–recovery trajectory. Bacterial richness (Chao1) decreased after planting, while evenness increased; Shannon diversity remained stable. Community composition shifted directionally, with higher relative abundance of Pseudomonadota (formerly Proteobacteria) and reduced Acidobacteriota at later stages. PERMANOVA based on Bray–Curtis distances indicated significant temporal differences in community structure. RDA indicated that soil organic matter and bulk density were the primary drivers of community structural variation. Functionally, the overall metabolic framework remained stable, whereas pathways related to genetic information processing and metabolism exhibited significant differences (p < 0.05). By examining both intra-annual dynamics and inter-annual changes in soil bacteria and physicochemical properties following the planting of ‘Yitong 2’, this study clarifies patterns of soil property variation and trajectories of microbial community structure and functional potential, thereby providing a scientific basis for the establishment of high-quality I. polycarpa plantations and the sustainable development of soil ecosystems. Full article

(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

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18 pages, 9278 KB

Open AccessArticle

Integrated Metagenomic and Metabolomic Analyses Reveal Rhizosphere Soil Microecological Changes in Thlaspi arvense L. Lines with Different Alkaloid Contents

by Wenjie Zhang, Chao Fan, Lie Yang, Yan Sun and Lili Tang

Microorganisms 2026, 14(3), 643; https://doi.org/10.3390/microorganisms14030643 - 12 Mar 2026

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Abstract

Pennycress (Thlaspi arvense L.), a representative and economically valuable cover crop, supports and enhances key ecological processes throughout its life cycle via its root system. It is hypothesized that pennycress selectively modulates its rhizosphere microbial community through root-derived metabolites, which may influence [...] Read more.

Pennycress (Thlaspi arvense L.), a representative and economically valuable cover crop, supports and enhances key ecological processes throughout its life cycle via its root system. It is hypothesized that pennycress selectively modulates its rhizosphere microbial community through root-derived metabolites, which may influence both the crop’s growth and the subsequent crops in rotation. However, systematic investigations comparing the rhizosphere microbiomes and metabolomes among different pennycress lines remain limited. This study employed metagenomic and metabolomic approaches to examine the dynamic changes in the rhizosphere microbial community and metabolite profiles of three pennycress lines with significantly different total alkaloid contents. The goal was to elucidate the interactions between microbes and metabolites. Results indicated significant differences in microbial community structure across the cultivars. JiL67 maintained stable community diversity, while LiN54 (with the lowest alkaloid content) showed reduced diversity. HeL43 (with the highest alkaloid content) exhibited increased diversity but also potential community homogenization, accompanied by the significant enrichment of microbial taxa capable of alkaloid tolerance. Metabolomic analysis identified metabolites such as Portulacaxanthin II, Oleanolic acid, and Soraphen A as significantly enriched in the rhizosphere soil of pennycress. This study reveals the shifts in rhizosphere microbial communities and metabolites linked to different pennycress lines and uncovers their interactive mechanisms, providing a scientific foundation for developing more economically efficient pennycress cultivation strategies. Full article

(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

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28 pages, 5943 KB

Open AccessArticle

The Driving Mechanisms of Soil Microbial Community Diversity and Stability in Different Plant Communities Along the Lower Jinsha River’s Water-Level-Fluctuation Zone

by Jingying Lu, Yuehua Zhang, Xianyong Dong, Xiaogang Wu, Lumei Xiao, Kaiwen Pan, Lin Zhang and Juan Wang

Microorganisms 2026, 14(3), 604; https://doi.org/10.3390/microorganisms14030604 - 9 Mar 2026

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Abstract

The Water-Level-Fluctuation Zones (WLFZ) of the Lower Jinsha River, as a typical transition areas between land and water, show crucial ecological functions. However, the relationship between soil nutrients and microbial communities in different plant communities of the WLFZ is poorly understand. Therefore, we [...] Read more.

The Water-Level-Fluctuation Zones (WLFZ) of the Lower Jinsha River, as a typical transition areas between land and water, show crucial ecological functions. However, the relationship between soil nutrients and microbial communities in different plant communities of the WLFZ is poorly understand. Therefore, we chose four typical plant communities, including Parthenium hysterophorus (P. hysterophorus), Ziziphus mauritiana (Z. mauritiana), Cynodon dactylon (C. dactylon), Zea mays (Z. mays), as a long-term plant communities experiment-monitoring site in a WLFZ of the Lower Jinsha River. By using high-throughput sequences, Mantel test and Mediation model, we explored the changing characteristics of soil nutrients and microbial communities, especially bacteria and fungi, and their driving role in the microbial stability in four typical plant communities. The results indicated that soil properties and enzyme activities noticeably changed among four types of different plant communities in the WLFZ, of which their P. hysterophorus and Z. mauritiana treatments were eventually higher than their of Z. mays and C. dactylon treatments. In the bacteria and fungi communities, the OTU number of P. hysterophorus and Z. mauritiana treatments were higher than their of C. dactylon and Z. mays treatments, which showed that the bacterial biomarkers only explained with the order, but the fungal biomarkers could explain with species. The bacterial and fungal diversity among four types of different plant communities in the WLFZ significantly changed such that the bacterial and fungal explanations of principal coordinate analysis (PCoA) was at 42.45% and 28.17%, respectively, and the anosim analysis of bacteria and fungi showed the p was 0.001 and the R was at 0.6995 and 0.7491. The bacterial and fungal co-occurrence network patterns presented that the bacterial community structure of the C. dactylon and P. hysterophorus treatments were the most complicated under the Z. mauritiana and Z. mays treatments, whereas the communities stability of C. dactylon and P. hysterophorus treatments were notably lower than that of their Z. mauritiana and Z. mays treatments. Lastly, the CCA, mantel test and intermediary analysis indicated pH served as the primary direct driver in the Z. mauritiana community, soil moisture exerted dominant effects in Z. mays and P. hysterophorus, while in C. dactylon, bacterial stability was indirectly modulated by pH mediated through SMC changes. This study highlights the major role of soil nutrients and enzyme activities in driving ecosystem stability of bacterial and fungal communities in four different plant communities in the WLFZ. Full article

(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

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21 pages, 1856 KB

Open AccessArticle

Draft Genome Sequence of Bacillus sp. Strain 11B20, a Promising Plant-Growth Promoting Bacterium Associated with Maize (Zea mays L.) in the Yaqui Valley, Mexico

by Alina Escalante-Beltrán, Pamela Helué Morales-Sandoval, Amelia Cristina Montoya-Martínez, Edgar A. Cubedo-Ruíz, Rubén Félix-Gastélum, Fannie Isela Parra-Cota and Sergio de los Santos-Villalobos

Microorganisms 2026, 14(2), 485; https://doi.org/10.3390/microorganisms14020485 - 17 Feb 2026

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Abstract

Strain 11B20 was isolated from a commercial field of maize (Zea mays L.) located in the Yaqui Valley, Mexico. The draft genome sequence revealed a genomic size of 3,759,824 bp, 41.6% G + C content, 973,288 bp N50, 2 L50, and 29 [...] Read more.

Strain 11B20 was isolated from a commercial field of maize (Zea mays L.) located in the Yaqui Valley, Mexico. The draft genome sequence revealed a genomic size of 3,759,824 bp, 41.6% G + C content, 973,288 bp N50, 2 L50, and 29 contigs. According to the 16S rRNA gene, strain 11B20 belongs to the genus Bacillus. Genome annotation revealed 3952 coding DNA sequences (CDSs) grouped into 319 subsystems. Among these, several CDSs were associated with traits related to plant growth promotion, including (i) virulence, disease, and defense (33 CDSs); (ii) iron acquisition and metabolism (28 CDSs); and (iii) secondary metabolism (6 CDSs), among others. In vitro, metabolic analysis (IAA, siderophore biosynthesis; phosphorus solubilization; and tolerance to thermal, hydric, and saline stress) confirmed the genomic background of this strain. Finally, in planta assays showed that the inoculation of Bacillus sp. 11B20 significantly (p ≤ 0.05) increased the root length (48.2%) and root dry weight (35.4%) versus non-inoculated maize plants. Thus, this is the first report of Bacillus sp. 11B20 as a promising beneficial strain for sustainable corn production, and further research is needed to ensure the success of the application of this strain in agriculture. Full article

(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

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20 pages, 7060 KB

Open AccessArticle

Tree Species Mixing Regulates Soil Multi-Nutrient Cycling by Altering Microbial Network Complexity and Assembly Processes in Larix olgensis

by Yue Liu, Chunjing Jiao, Wanju Feng, Yuchun Yang, Bing Yang, Fang Wang and Jun Wang

Microorganisms 2026, 14(2), 388; https://doi.org/10.3390/microorganisms14020388 - 6 Feb 2026

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Abstract

Establishing mixed conifer–broadleaf forests enhances soil multi-nutrient cycling (SMC), yet the underlying mechanisms, particularly the role of rhizosphere microbial communities, remain poorly understood. This study investigated how bacterial and fungal communities in the rhizosphere soil of Larix olgensis drive SMC in both pure [...] Read more.

Establishing mixed conifer–broadleaf forests enhances soil multi-nutrient cycling (SMC), yet the underlying mechanisms, particularly the role of rhizosphere microbial communities, remain poorly understood. This study investigated how bacterial and fungal communities in the rhizosphere soil of Larix olgensis drive SMC in both pure and mixed plantations with Fraxinus mandshurica, elucidating the microbial pathways for nutrient supply in mixed stands. Our results indicated that SMC in the L. olgensis rhizosphere soil was significantly greater in mixed stands (0.43) than in pure stands (−0.51). Tree species mixing significantly enhanced microbial diversity, increased the stochasticity of community assembly, and reduced dispersal limitation. Cross-kingdom (bacteria–fungi) co-occurrence networks in mixed stands showed a 19.7% increase in positive correlations, indicating stronger microbial cooperation. Random forest analysis identified microbial diversity, network complexity, and bacterial assembly processes as the main predictors of SMC. Structural equation modeling indicated that microbial diversity indirectly promoted SMC via increased network complexity, while bacterial assembly processes directly influenced SMC. These findings demonstrate that mixed conifer–broadleaf plantations improve soil microbial functioning and nutrient cycling by modifying microbial diversity, assembly processes, and interaction networks. Full article

(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

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19 pages, 5700 KB

Open AccessArticle

Bacterial Community Structure and Environmental Adaptation in the Endorhizosphere and Rhizosphere Soils of Aeluropus sinensis from Saline Lands Across Coastal and Inland Regions of China

by Luoyan Zhang, Saiyu Han, Xiuxiu Guo, Lijie Wang, Yilin Fan, Xuejie Zhang and Shoujin Fan

Microorganisms 2026, 14(1), 165; https://doi.org/10.3390/microorganisms14010165 - 12 Jan 2026

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Abstract

Bacterial communities in the rhizosphere and endorhizosphere of plants show distinct composition, function, and ecological roles during adaptation to diverse habitats. This study examines how rhizosphere and endophytic microbes associated with Aeluropus sinensis—a salt-excreting halophyte—contribute to its salt tolerance across saline-alkali environments. [...] Read more.

Bacterial communities in the rhizosphere and endorhizosphere of plants show distinct composition, function, and ecological roles during adaptation to diverse habitats. This study examines how rhizosphere and endophytic microbes associated with Aeluropus sinensis—a salt-excreting halophyte—contribute to its salt tolerance across saline-alkali environments. Microbial diversity and composition were analyzed via 16S rRNA gene amplicon sequencing. Soil physicochemical properties were measured to evaluate environmental effects. Linear regression assessed microbial–environment relationships, and co-occurrence networks identified key taxa and their adaptive strategies along environmental gradients. Soil salinity significantly affected rhizosphere bacterial diversity, with moderate levels increasing richness. Proteobacteria dominated both root and rhizosphere microbiomes across habitats. The endorhizosphere community strongly correlated with soil nutrients such as available phosphorus (AP) and total nitrogen (TN). Co-occurrence analysis reveals that chemoheterotrophic microbes in the A. sinensis rhizosphere employ distinct adaptive strategies across gradients, and ammonia-oxidizing bacteria (AOB) may support nitrogen cycling in the Yellow River Delta saline–alkaline ecosystem. This study underscores microbial adaptability in salt-tolerant grasses, demonstrating that comparing rhizosphere and endorhizosphere microbiomes in Poaceae under stress improves understanding of microbial functions in harsh environments. Full article

(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

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16 pages, 3393 KB

Open AccessArticle

Effects of Different Crop Rotations on Microbial Diversity and Enzyme Activities in Brassica napus Rhizosphere Soil

by Xiaona Tian, Jia Duan, Hongli Huo, Jiuru Huangfu, Mengjiao Yan, Huilin Lu, Ziqin Li and Peiling Song

Microorganisms 2026, 14(1), 91; https://doi.org/10.3390/microorganisms14010091 - 31 Dec 2025

Cited by 1 | Viewed by 668

Abstract

Continuous cropping of Brassica napus impairs sustainable production via soil nutrient imbalance and microecological degradation. We evaluated rhizosphere soil properties and microbial communities under rotations crops (Triticum aestivum [TaBn], Beta vulgaris [BvBn], Glycine max [GmBn], Sorghum bicolor [SbBn], Hordeum vulgare [HvBn], and [...] Read more.

Continuous cropping of Brassica napus impairs sustainable production via soil nutrient imbalance and microecological degradation. We evaluated rhizosphere soil properties and microbial communities under rotations crops (Triticum aestivum [TaBn], Beta vulgaris [BvBn], Glycine max [GmBn], Sorghum bicolor [SbBn], Hordeum vulgare [HvBn], and Brassica napus [BnBn]). BvBn had the highest total nitrogen, total potassium, available potassium, and organic matter contents. TaBn exhibited the highest soil enzyme activities, and its bacterial/fungal Chao1/Simpson indices and unique operational taxonomic units (OTUs; bacteria: 333, fungi: 37) exceeded other patterns. Principal coordinate analysis showed distinct microbial community separation in BvBn/TaBn versus BnBn. TaBn enriched dominant bacterial phyla Pseudomonadota and Actinomycetota; all preceding crops increased fungal phylum Ascomycota while reducing Mucoromycota. Comprehensive assessment confirmed all preceding crops, except oilseed rape altered rhizosphere microbial structure, with TaBn as the optimal preceding crops. Full article

(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

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21 pages, 6874 KB

Open AccessArticle

Responses of Soil Microbial Communities and Anthracnose Dynamics to Different Planting Patterns in Dalbergia odorifera

by Long Xu, Kexu Long, Yichi Zhang, Guoying Zhou and Junang Liu

Microorganisms 2025, 13(12), 2876; https://doi.org/10.3390/microorganisms13122876 - 18 Dec 2025

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Abstract

Anthracnose is one of the major diseases affecting Dalbergia odorifera T. Chen. However, the soil microbial mechanisms underlying D. odorifera responses to anthracnose remain largely unexplored. This study investigated three planting systems: a Dalbergia odorifera monoculture (J); a mixed plantation of D. odorifera [...] Read more.

Anthracnose is one of the major diseases affecting Dalbergia odorifera T. Chen. However, the soil microbial mechanisms underlying D. odorifera responses to anthracnose remain largely unexplored. This study investigated three planting systems: a Dalbergia odorifera monoculture (J); a mixed plantation of D. odorifera and Pterocarpus macrocarpus (JD); and a composite mixed plantation of D. odorifera, P. macrocarpus, and Clinacanthus nutans (JDY). Using amplicon sequencing technology for soil microbial analysis and combining soil physical and chemical properties with disease severity, we comprehensively analyzed changes in soil microbial community structure and function across different planting modes. The results showed that the diverse mixed mode (JD, JDY) significantly improved soil physicochemical properties and promoted soil nutrient cycling. Redundancy analysis (RDA) indicated that soil organic matter (SOM) and disease severity, quantified by the area under the disease progress curve (AUDPC), were the primary environmental drivers of microbial community variation. Genera positively correlated with SOM and negatively correlated with AUDPC were significantly enriched in JDY and JD, whereas genera showing opposite relationships were predominantly enriched in J. Functional predictions revealed enhanced nutrient-cycling capacities in JD and JDY, with JDY uniquely harboring functional groups such as Arbuscular Mycorrhizal, Epiphyte, and Lichenized taxa. In contrast, microbial functions in the J plantation were mainly limited to environmental amelioration. Co-occurrence network analysis further showed that as planting patterns shifted from J to JDY, microbial communities evolved from competition-dominated networks to cooperative defensive networks, integrating efficient decomposition with strong pathogen suppression potential. The study demonstrates that complex mixed planting systems regulate soil properties, enhance the enrichment of key functional microbial taxa, reshape community structure and function, and ultimately enable ecological control of anthracnose disease. This study provides new perspectives and theoretical foundations for ecological disease management in plantations of rare tree species and for microbiome-based ecological immunization strategies. Full article

(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

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15 pages, 7642 KB

Open AccessArticle

Effects of Endophytic Fungi and Arbuscular Mycorrhizal Fungi on Microbial Community Function and Metabolic Pathways in the Rhizosphere Soil of Festuca rubra

by Zhengming Luo, Yanying Zhou, Xuerong Wang, Lei He and Tong Jia

Microorganisms 2025, 13(12), 2735; https://doi.org/10.3390/microorganisms13122735 - 30 Nov 2025

Cited by 1 | Viewed by 745

Abstract

Numerous studies have shown that there are many uncertainties associated with the interactions of nitrogen with plants and microorganisms. In particular, the effects of symbioses between plants and various microorganisms on soil microbial community function remain unclear. Metagenomic sequencing was used to explore [...] Read more.

Numerous studies have shown that there are many uncertainties associated with the interactions of nitrogen with plants and microorganisms. In particular, the effects of symbioses between plants and various microorganisms on soil microbial community function remain unclear. Metagenomic sequencing was used to explore the changes in microbial community composition, function and metabolic pathways in rhizosphere soil and the associated influencing factors under different nitrogen levels caused by arbuscular mycorrhizal fungi (AMF) inoculation of F. rubra infected with endophytic fungi and nonendophytic fungi. Plant nutrient allocation (aboveground/belowground), soil pH, and enzymatic activities significantly modulated the functional profiles of the bacterial, fungal, and archaeal communities within these rhizospheres. Soil β-glucosidase activity had the greatest effect on the cluster of orthologous groups of proteins (COG) function of the rhizosphere soil bacterial community, and soil L-leucine aminopeptidase had the greatest effect on the COG function of the rhizosphere soil fungal and archaeal communities. The contributions of AMF colonization to the kyoto encyclopedia of genes and genomes (KEGG) functions of bacteria and archaea in the rhizosphere soil were greater than those of F. rubra infection with endophytic fungi, and AMF colonization improved the metabolic pathways, secondary metabolite biosynthesis, microbial metabolism, amino acid biosynthesis and carbon metabolism of bacterial and archaeal communities in the rhizosphere soil of F. rubra. The effects of endophytic fungi and AMFs on the function and metabolic pathways of symbiotic rhizosphere soil microbial communities were heterogeneous. This study revealed that considering both biotic and abiotic factors is essential for predicting the maintenance of soil ecosystem function by plant–fungal symbionts. Full article

(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

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21 pages, 1667 KB

Open AccessArticle

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

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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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18 pages, 330 KB

Open AccessArticle

Bacterial Isolates from Avocado Orchards with Different Agronomic Management Systems with Potential for Promoting Plant Growth in Tomate and Phytopathogen Control

by Adilene Velázquez-Medina, Evangelina Esmeralda Quiñones-Aguilar, Ernestina Gutiérrez-Vázquez, Nuria Gómez-Dorantes, Gabriel Rincón-Enríquez and Luis López-Pérez

Microorganisms 2025, 13(9), 1974; https://doi.org/10.3390/microorganisms13091974 - 23 Aug 2025

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Abstract

The bacterial diversity of soils cultivated with avocado (Persea americana M.) is influenced by different factors, perhaps the most decisive being the type of agronomic management used by farmers. In conventional agronomic management (CM), high doses of agrochemicals are applied, in contrast [...] Read more.

The bacterial diversity of soils cultivated with avocado (Persea americana M.) is influenced by different factors, perhaps the most decisive being the type of agronomic management used by farmers. In conventional agronomic management (CM), high doses of agrochemicals are applied, in contrast to organic agronomic management (OM), where organic fertilizers are used. This alters the diversity and abundance of soil microorganism populations, which in turn affects crop health. This study aimed to isolate and morphologically characterize rhizospheric bacteria from avocado trees under different agronomic management systems (CM and OM). For the bacterial isolates, their ability to promote plant growth in vitro was determined through biochemical tests for phosphorus and calcium solubilization and nitrogen fixation. In addition, their in vivo effect on tomato (S. lycopersicum) growth was evaluated, and their antagonistic capacity against Fusarium sp. was assessed. The results showed differences in the quantity, diversity, and morphologies of bacterial isolates depending on the type of agronomic management. A higher Shannon diversity index was found in OM (2.44) compared to CM (1.75). A total of 35 bacterial isolates were obtained from both management types. A greater number of isolates from OM soils exhibited in vitro PGP activity; notably, eight isolates from OM plots showed phosphate-solubilizing activity, compared to only one from CM plots. Furthermore, although all isolates demonstrated nitrogen fixing capacity, those from OM orchards produced significantly higher nitrate levels than the control (Azospirillum vinelandii). On the other hand, inoculation of tomato plants with bacterial isolates from OM soils increased plant height, root length, and total fresh and dry biomass compared to isolates from CM soils. Likewise, OM isolates exhibited greater antagonistic activity against Fusarium sp. These findings demonstrate the impact of agronomic management on soil bacterial populations and its effect on plant growth and protection against pathogens. Full article

(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

Review

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Open AccessReview

Trichoderma: Dual Roles in Biocontrol and Plant Growth Promotion

by Xiaoyan Chen, Yuntong Lu, Xing Liu, Yunying Gu and Fei Li

Microorganisms 2025, 13(8), 1840; https://doi.org/10.3390/microorganisms13081840 - 7 Aug 2025

Cited by 23 | Viewed by 8137

Abstract

The genus Trichoderma plays a pivotal role in sustainable agriculture through its multifaceted contributions to plant health and productivity. This review explores Trichoderma’s biological functions, including its roles as a biocontrol agent, plant growth promoter, and stress resilience enhancer. By producing various [...] Read more.

The genus Trichoderma plays a pivotal role in sustainable agriculture through its multifaceted contributions to plant health and productivity. This review explores Trichoderma’s biological functions, including its roles as a biocontrol agent, plant growth promoter, and stress resilience enhancer. By producing various enzymes, secondary metabolites, and volatile organic compounds, Trichoderma effectively suppresses plant pathogens, promotes root development, and primes plant immune responses. This review details the evolutionary adaptations of Trichoderma, which has transitioned from saprotrophism to mycoparasitism and established beneficial symbiotic relationships with plants. It also highlights the ecological versatility of Trichoderma in colonizing plant roots and improving soil health, while emphasizing its role in mitigating both biotic and abiotic stressors. With increasing recognition as a biostimulant and biocontrol agent, Trichoderma has become a key player in reducing chemical inputs and advancing eco-friendly farming practices. This review addresses challenges such as strain selection, formulation stability, and regulatory hurdles and concludes by advocating for continued research to optimize Trichoderma’s applications in addressing climate change, enhancing food security, and promoting a sustainable agricultural future. Full article

(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

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