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Keywords = rhizosphere microbial community structure

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18 pages, 3919 KB  
Article
Long-Term No-Tillage Improves the Rhizosphere Microbial Community of Maize by Enhancing Root Development and Soil Nutrients
by Lina Dong, Xiangfei Han, Shuaimin Chen, Yanjie Lv, Jinyu Zheng, Yang Luo, Yongjun Wang and Lichun Wang
Agronomy 2026, 16(11), 1037; https://doi.org/10.3390/agronomy16111037 (registering DOI) - 23 May 2026
Abstract
Tillage practices can change the soil environment (including soil properties and enzyme activity) and the rhizosphere microbial community, thereby inducing changes in root growth and the nutrient uptake capacity. This study was carried out on a long-term (since 1983) tillage field experimental platform. [...] Read more.
Tillage practices can change the soil environment (including soil properties and enzyme activity) and the rhizosphere microbial community, thereby inducing changes in root growth and the nutrient uptake capacity. This study was carried out on a long-term (since 1983) tillage field experimental platform. It aimed to explore the effects of tillage practices and growth stages on maize root development, soil properties, and the rhizosphere microbial community. The results can provide a theoretical basis for the further analysis of crop–soil–microbial interactions. In our study, we investigated the abundance and diversity of the rhizosphere microbial community and their relationship with root growth characteristics and soil factors under long-term (since 1983) conventional tillage (CT), subsoil tillage (ST), and no-tillage (NT) practices using quantitative PCR and high-throughput 16S/ITS sequencing. In 2020, at the 30-days-after-silking (VT 30) stage, NT increased the root length, root dry weight, N accumulation, and N uptake rate of maize roots compared with CT by 16.7%, 16.3%, 41.9%, and 41.9%, respectively. In 2020, at the 12th leaf (V12) and VT 30 stages of maize, NT significantly increased the contents of soil total nitrogen (by 16.3% and 11.0%, respectively), total carbon (by 23.9% and 12.9%, respectively), soil organic matter (by 24.8% and 10.3%, respectively), and soil urease activity (by 5.5% and 5.6%, respectively) compared with CT. Moreover, NT significantly increased the bacterial and fungal abundances compared with CT. Redundancy analysis (RDA) showed that the variation in the microbial structure correlated markedly with the alteration in root indicators, soil properties, and enzyme activities. Long-term no-tillage improved the abundance and diversity of rhizosphere microbial communities by increasing the soil total nitrogen, total carbon, and soil organic matter, and promoted the N accumulation of roots and their uptake rate. Full article
(This article belongs to the Section Agroecology Innovation: Achieving System Resilience)
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18 pages, 3293 KB  
Article
Metagenomic Insights into Regional Differences in the Rhizosphere Microbial Communities of Stellera chamaejasme L. in Inner Mongolia
by Zeyu Pan, Jian Bao, Xiangdong Liu, Gentu Ge and Muqier Zhao
Microorganisms 2026, 14(6), 1167; https://doi.org/10.3390/microorganisms14061167 - 22 May 2026
Viewed by 55
Abstract
Rhizosphere microorganisms are important components of grassland ecosystems, but the rhizosphere microbiome of the poisonous and medicinal plant Stellera chamaejasme L. remains poorly characterized. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition, community structure, differentially enriched taxa, and [...] Read more.
Rhizosphere microorganisms are important components of grassland ecosystems, but the rhizosphere microbiome of the poisonous and medicinal plant Stellera chamaejasme L. remains poorly characterized. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition, community structure, differentially enriched taxa, and KEGG-based functional potential of rhizosphere microbial communities associated with S. chamaejasme from three typical steppe regions in Inner Mongolia. Acidobacteria, Proteobacteria, and Actinobacteria were the dominant phyla, while Sphingomonas, Bradyrhizobium, and Streptomyces were among the dominant genera. Genus-level profiles and ordination analysis showed region-associated community patterns, and rarefaction curves indicated that sequencing depth was sufficient to capture most detectable taxa. LEfSe analysis identified region-associated differentially enriched taxa, including Sphingomonas-, Bradyrhizobium/Nitrospira-, and Streptomyces/Solirubrobacter-associated taxa. KEGG annotation suggested broadly similar major functional categories across regions, with some differences in the relative abundance of metabolic pathways. These results provide baseline metagenomic information on S. chamaejasme rhizosphere communities. Because of the limited replication and lack of soil physicochemical measurements, ecological mechanisms should be tested in future studies. Full article
(This article belongs to the Section Plant Microbe Interactions)
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19 pages, 1983 KB  
Article
Synergistic Remediation of Cd/Pb-Contaminated Construction and Demolition Waste Landfill Soil: Roles of Soil Amendments, Plant Selection, and Microbial Community Restructuring
by Jiangqiao Bao, Yisong Wei, Ying Ren, Hao Chen, Hongzhi He and Zhengjun Shi
Agronomy 2026, 16(10), 1017; https://doi.org/10.3390/agronomy16101017 - 21 May 2026
Viewed by 69
Abstract
Cadmium (Cd) and lead (Pb) co-contamination in construction and demolition waste landfill soils presents a significant challenge to ecosystem health, necessitating effective remediation strategies. This study investigated a synergistic approach combining a composite amendment (compost, superphosphate, desulfurized gypsum) with seven plant species to [...] Read more.
Cadmium (Cd) and lead (Pb) co-contamination in construction and demolition waste landfill soils presents a significant challenge to ecosystem health, necessitating effective remediation strategies. This study investigated a synergistic approach combining a composite amendment (compost, superphosphate, desulfurized gypsum) with seven plant species to elucidate the interactions driving metal immobilization and phytoextraction. The amendment significantly altered soil properties: it reduced total Cd while increasing its bioavailability, and enhanced soil fertility (e.g., elevated organic matter and total nitrogen). Plant responses varied: Solanum americanum Mill. and Tagetes patula L. exhibited high Cd phytoextraction capacity, whereas Lolium perenne L. sequestered Cd/Pb primarily in roots. The bacterial community shifted from an oligotrophic, stress-tolerant state (e.g., Sphingomonas-dominated) in contaminated soil to a copiotrophic, functionally active state (e.g., Streptomyces-enriched) in amended soil. Community structure was strongly correlated with available Cd, pH, and nutrient levels. Key microbial biomarkers were specifically enriched in different plant rhizospheres. In contrast, the fungal community exhibited minimal responsiveness. These findings demonstrate that remediation efficiency is governed by an integrated “amendment–plant–microbe” framework: amendments regulate metal bioavailability, plants execute extraction or stabilization, and the restructured microbiome supports nutrient cycling and plant health. This integrated remediation strategy directly supports the Sustainable Development Goals of the 2030 Agenda, especially on environmentally sound management of chemicals and wastes and land degradation neutrality. This mechanistic understanding underscores the necessity of combined biological and chemical strategies for sustainable remediation of co-contaminated soils, ultimately enabling ecological reclamation and safe recycling of such urban marginal lands into productive uses. Full article
(This article belongs to the Special Issue Soil Improvement and Restoration)
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18 pages, 3291 KB  
Article
Differential Response of Microbial Necromass Carbon in Rhizospheric and Non-Rhizospheric Soil to Mulching Measures and How It Drives C Sequestration Mechanism on Loess Plateau
by Jiaqi Hao, Yufei Gao, Ni Chen and Xing Wang
Agronomy 2026, 16(10), 1010; https://doi.org/10.3390/agronomy16101010 - 21 May 2026
Viewed by 118
Abstract
Microbial necromass carbon (MNC) is recognized as an important and relatively stable component of soil organic carbon (SOC); however, it is often overlooked and poorly understood in soil management practices, particularly in the context of Loess Plateau farmlands. Here, a 13-year field experiment [...] Read more.
Microbial necromass carbon (MNC) is recognized as an important and relatively stable component of soil organic carbon (SOC); however, it is often overlooked and poorly understood in soil management practices, particularly in the context of Loess Plateau farmlands. Here, a 13-year field experiment was carried out to examine the differences in MNC distribution, the role of MNC in SOC storage, and the impact of environmental factors under long-term mulching practices. The experiment used four treatments: (1) no mulching (NT), (2) straw mulching (NSM), (3) plastic mulching (NPM), and (4) ridge mulching (NRM). Compared to NT, all mulching methods increased SOC levels, phospholipid fatty acids (PLFAs), and amino sugar (AS) content. Straw mulching enhanced microbial biomass carbon (MBC), reduced the gap in AS content between rhizosphere and non-rhizosphere soils, and significantly increased MNC. Conversely, NPM and NRM primarily increased MBC and MNC within the rhizosphere soil. Generally, the rhizosphere soil had higher AS content than non-rhizosphere soil. However, regarding the proportion of MNC contributing to SOC, non-rhizosphere soil showed a significantly greater contribution than rhizosphere soil (p < 0.05). The contribution of MNC to SOC ranged from 10.70% to 26.38% under different treatments. Fungal-derived MNC generally contributed more to SOC (7.96–19.73%) than bacterial-derived MNC (2.62–6.65%). Soil temperature, the C/N ratio, pH, and total phosphorus influence microbial community structure and MBC, which in turn affect MNC and regulate SOC. These results enhance our understanding of how agricultural management practices on the Loess Plateau affect carbon sequestration. Full article
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23 pages, 5603 KB  
Article
Gradient Potassium Application Differentially Regulates Rhizosphere Bacterial and Fungal Communities in Cherry Tomato (Solanum lycopersicum var. cerasiforme)
by Chenpeng Gao, Guigui Wan, Ruifeng Cheng, Quansheng Li, Qinglu Fan, Jinxia Cui and Linnan Wu
Plants 2026, 15(10), 1545; https://doi.org/10.3390/plants15101545 - 19 May 2026
Viewed by 161
Abstract
Potassium (K) is an essential macronutrient for plants and plays a critical role in soil microbial processes. However, its systemic effects on rhizosphere microorganisms in high-value crops like cherry tomato remain poorly understood. This study established a potassium gradient (K0 represents the no-potassium [...] Read more.
Potassium (K) is an essential macronutrient for plants and plays a critical role in soil microbial processes. However, its systemic effects on rhizosphere microorganisms in high-value crops like cherry tomato remain poorly understood. This study established a potassium gradient (K0 represents the no-potassium application, K1 represents low-potassium application, K2 represents a moderate-potassium application, K3 represents the conventional-potassium application, and K4 represents excessive-potassium application) to investigate responses in growth and rhizosphere bacterial and fungal communities of cherry tomato. Moderate potassium (K2) significantly enhanced dry matter accumulation in cherry tomato. Bacterial and fungal communities displayed distinct patterns: bacterial structure shifted continuously along the gradient, with specific enrichment of functional genera (nitrogen-fixing Ensifer, biocontrol-related Lysobacter), increased unique OTUs, and gradual co-occurrence network optimization at K2. In contrast, fungal community composition and network structure showed threshold responses to potassium. Low K (K1) suppressed dominant Ascomycota and increased unclassified fungi, while high potassium (K4) enriched parasitic/pathogenic fungi (Alternaria, Curvularia), increased network modularity, and reduced stability. This microbial ecological perspective highlights that optimized potassium application regulates functional microorganisms and differentially shapes rhizosphere communities, providing a theoretical basis for precision potassium management in cherry tomato. Full article
(This article belongs to the Section Plant Protection and Biotic Interactions)
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18 pages, 2654 KB  
Article
Soil Nematode Community Composition and Energy Structure in the Root Zones of Woody Plants in the Ili River Valley: A Comparison Between Near-Pure-Species Trees and Mixed Shrub Communities
by Yijing Lv, Junyan Fan, Deshuai Sun, Suqing Li, Shuyue Fang, Cuiling Ye and Xiaolan Li
Forests 2026, 17(5), 599; https://doi.org/10.3390/f17050599 - 15 May 2026
Viewed by 219
Abstract
As a typical mountain ecosystem in the western Tianshan Mountains, the Ili River Valley possesses abundant vegetation resources. Soil nematodes are effective biological indicators for evaluating soil micro-food webs. Nevertheless, the response mechanisms of nematode community structure to distinct vegetation types, especially native [...] Read more.
As a typical mountain ecosystem in the western Tianshan Mountains, the Ili River Valley possesses abundant vegetation resources. Soil nematodes are effective biological indicators for evaluating soil micro-food webs. Nevertheless, the response mechanisms of nematode community structure to distinct vegetation types, especially native trees and forest-edge shrubs, remain poorly understood in this region. In this study, two dominant tree species (Picea schrenkiana and Malus sieversii) and two forest-edge shrub species (Berberis heteropoda and Berberis sibirica) were investigated. We analyzed the composition, diversity, and energy structure of rhizosphere soil nematodes and further compared their differences among plant species. The results indicated that tree rhizospheres had significantly higher amounts of nitrate nitrogen (NO3-N and microbial biomass carbon (MBC), along with a lower amount of extractable organic carbon/extractable total nitrogen (EOC:ETN) than shrub rhizospheres (p < 0.05). Picea schrenkiana (PS) exhibited greater root carbon storage, higher root biomass, and a higher root carbon-to-nitrogen ratio (RC:RN) than Berberis heteropoda (BH) and Berberis sibirica (BS) (p < 0.05). The genus Chiloplacus dominated the nematode community across all four woody plants. The relative abundance of omnivore-predatory nematodes was markedly higher in shrubs (BH and BS) than in trees (PS and MS). The soil food webs of PS and MS were degraded, whereas shrub food webs were in a transitional state between structured and degraded habitats. Shrubs presented a higher maturity index, structural metabolic footprint, and energy flux of omnivore-predatory nematodes, but a lower energy flux of bacterivorous nematodes. Additionally, PS had the highest nematode carbon use efficiency (NCUE) and the lowest energy flux uniformity (U). NO3-N extractable total nitrogen (ETN), soil organic carbon (SOC), and root traits were the primary factors driving variations in nematode communities and carbon indicators. Therefore, nematode carbon indicators closely associated with soil carbon and nitrogen cycling have the potential to serve as sensitive auxiliary biological metrics for evaluating material cycling and energy flow in pure forests and shrub ecosystems. This study provides empirical support for the assessment of regional ecosystem stability. Full article
(This article belongs to the Section Forest Soil)
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24 pages, 4092 KB  
Article
Biomass Seedling Trays Drive Rhizosphere Microbiome Restructuring and PGPR Enrichment in Tomato
by Jiayun Zhang, Xiangyu Zhang and Qiang Chen
Plants 2026, 15(10), 1486; https://doi.org/10.3390/plants15101486 - 13 May 2026
Viewed by 247
Abstract
Tomato (Solanum lycopersicum) is a globally important high-value cash crop. However, long-term continuous cropping causes frequent soil-borne diseases and soil microecological imbalance, while overreliance on chemical pesticides leads to pesticide residues and water eutrophication. Plant growth-promoting rhizobacteria (PGPR) are key resources [...] Read more.
Tomato (Solanum lycopersicum) is a globally important high-value cash crop. However, long-term continuous cropping causes frequent soil-borne diseases and soil microecological imbalance, while overreliance on chemical pesticides leads to pesticide residues and water eutrophication. Plant growth-promoting rhizobacteria (PGPR) are key resources for addressing tomato cultivation challenges, with their functions partly depending on the rhizosphere microenvironment inherently shaped by seedling tray materials. Using rhizosphere soil and substrates of tomato at different growth stages under biomass (BM) and plastic (PM) seedling tray treatments, this study combined culture-independent and culture-dependent techniques to analyze microbial community characteristics and screen high-efficiency PGPR. Results showed that pH and available nitrogen drove microbial community assembly. BM significantly enriched beneficial taxa (e.g., Trichoderma and Bacillus) and enhanced culturable microbial abundance and genetic diversity, while PM enriched potential pathogens (e.g., Fusarium and Pyrenochaeta). The multifunctional strain S25095 from BM, with phosphate-solubilizing, potassium-solubilizing, and indole-3-acetic acid (IAA)-producing abilities, significantly promoted tomato shoot and root growth, outperforming single-functional strains and synthetic consortia. This study reveals the effects of growth stages and seedling tray treatments on tomato rhizosphere microorganisms, providing valuable PGPR resources for tomato cultivation. Full article
(This article belongs to the Section Plant Protection and Biotic Interactions)
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17 pages, 17107 KB  
Article
Rhizosphere Microbial Effects on Soil Quality of Pinus massoniana and Schima superba Mixed Plantations
by Wenyue Wang, Wei Yang, Wenqing Song, Shengyi Huang, Jianming Lai, Zhichun Zhou, Pengcheng Wang and Bin Wang
Plants 2026, 15(10), 1482; https://doi.org/10.3390/plants15101482 - 12 May 2026
Viewed by 342
Abstract
This study aimed to reveal the rhizosphere microbial community structure, carbon–nitrogen–phosphorus (C-N-P) nutrient cycling processes, and functional gene characteristics of Pinus massoniana and Schima superba in mixed forests. Furthermore, we sought to elucidate the microbial mechanisms by which mixed-species afforestation enhances soil quality [...] Read more.
This study aimed to reveal the rhizosphere microbial community structure, carbon–nitrogen–phosphorus (C-N-P) nutrient cycling processes, and functional gene characteristics of Pinus massoniana and Schima superba in mixed forests. Furthermore, we sought to elucidate the microbial mechanisms by which mixed-species afforestation enhances soil quality improvement, providing a theoretical basis in soil microbiology for the cultivation of these mixed forests. The research subjects included pure P. massoniana plantations (CLPs), pure S. superba plantations (CLSs), and individual P. massoniana (HJP) and S. superba (HJS) trees within mixed plantations (HJLs). We collected rhizosphere and bulk soil samples to analyze their physicochemical properties and enzyme activities. Metagenomic sequencing was employed to profile the rhizosphere microbial communities and functional genes involved in C-N-P cycling. Furthermore, by integrating a functional gene co-occurrence network analysis with structural equation modeling (SEM), we systematically elucidated the coupling relationships among the stand types, soil properties, microbial communities, and nutrient cycling. Mixed planting significantly improved soil quality; compared to the CLP and CLS forests, the nitrate nitrogen (NO3-N) content in the mixed forest soils increased by 121.01% and 120.10% (p < 0.05), and the activity of urease (URE) also significantly increased by 123.99% and 49.56%, respectively. Mixing significantly altered the microbial community structure. In the bacterial community of the mixed forests, the abundance of nitrogen-fixing and potentially phosphorus-solubilizing bacteria from the genera Paraburkholderia and Burkholderia increased. In the fungal community, the arbuscular mycorrhizal fungus Rhizophagus, which possesses a nutrient absorption advantage, exhibited absolute dominance, with its relative abundance ranging from 14.84% to 88.81%. The abundances of genes associated with denitrification and phosphorus starvation regulation were significantly upregulated in the mixed forests; notably, the abundance of phosphorus starvation regulation genes in the HJSs was 18.84% higher than that in the CLSs. A co-occurrence network analysis demonstrated that the proportion of positive correlation edges in the HJP nitrogen cycling network reached as high as 75.0%, and the average degree of the HJS phosphorus cycling network (2.691) surpassed that of the CLSs. The structural equation modeling further revealed that the association strength between the fungi and phosphorus cycling genes in the mixed forests increased to R2 = 0.915 (p < 0.01) from R2 = 0.213 in the pure forests. This mixed planting practice transforms nutrient cycling from a resource-competitive mode to a microbially synergized mode, thereby forming an efficient endogenous nutrient cycling system. This synergistic rhizosphere microbial effect is a key internal mechanism for overcoming nutrient bottlenecks and should serve as a diagnostic indicator of soil recovery in the ecological restoration of degraded pine forests. Full article
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21 pages, 2676 KB  
Article
Split Nitrogen Application Timing Steers Rhizosphere Nitrifiers and Nitrogen Utilization in Wheat
by Shuang Guo, Guanghui Yang, Wei Wu, Shuangshuang Liu, Yang Wang, Weiming Wang, Huasen Xu and Cheng Xue
Agriculture 2026, 16(9), 1006; https://doi.org/10.3390/agriculture16091006 - 3 May 2026
Viewed by 1071
Abstract
Split nitrogen (N) application is an important agronomic measure for improving wheat yield and quality, yet how rhizosphere nitrogen-transforming microbes respond to split N strategies and the underlying mechanisms remain unclear. This study investigated the effects of six N treatments, including control, basal [...] Read more.
Split nitrogen (N) application is an important agronomic measure for improving wheat yield and quality, yet how rhizosphere nitrogen-transforming microbes respond to split N strategies and the underlying mechanisms remain unclear. This study investigated the effects of six N treatments, including control, basal application, jointing-stage soil topdressing, and foliar applications at booting, anthesis, and 10 days post-anthesis, on the community structure and diversity of key rhizospheric nitrogen cyclers (ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB)) in wheat. Results showed that AOB and NOB alpha diversity were significantly modified by split N application. N application at anthesis enhanced AOB richness and diversity more than the later application, while concurrently decreasing NOB diversity. Booting-stage application enriched Nitrosospira and Nitrosomonas in the AOB community, whereas anthesis application increased Nitrososphaera sp. JG1 in AOA, but decreased Candidatus Nitrospira inopinata in NOB. Redundancy analysis identified soil pH, moisture, organic carbon, and key enzyme activities as the main drivers of microbial community assembly. Although no significant differences were observed in key agronomic traits among treatments, the 10 days post-anthesis treatment showed numerically superior yield and N uptake. Notably, AOB community evenness was significantly positively correlated with grain yield, protein yield, and N uptake, whereas NOB community diversity showed negative correlations. These findings demonstrate that split N application, particularly late foliar spray at 10 days post-anthesis, can modulate soil physico-chemical properties to selectively shape nitrogen-transforming microbial communities (notably AOB) in the wheat rhizosphere. This study provides a theoretical foundation for designing precise N management strategies rooted in rhizosphere ecology, with the goal of simultaneously improving yield, grain quality, and nitrogen use efficiency. Full article
(This article belongs to the Section Crop Production)
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16 pages, 4425 KB  
Article
Primary Succession Shifts Fine-Root Nutrient Acquisition from Morphological Capture to Rhizosphere-Mediated Biochemical Mobilization
by Qiao Gao, Gang Xu, Yi Hu, Meiyu Liu, Xuyang Lu and Baoli Duan
Forests 2026, 17(5), 555; https://doi.org/10.3390/f17050555 - 30 Apr 2026
Viewed by 237
Abstract
Primary succession following glacier retreat provides a natural system for testing whether soil development simply shifts fine roots along a single acquisitive–conservative axis orinstead changes the nutrient-acquisition pathway that dominates at the community level. We hypothesized a stage-dependent sequence, from substrate-limited exploration, to [...] Read more.
Primary succession following glacier retreat provides a natural system for testing whether soil development simply shifts fine roots along a single acquisitive–conservative axis orinstead changes the nutrient-acquisition pathway that dominates at the community level. We hypothesized a stage-dependent sequence, from substrate-limited exploration, to transient morphological capture, and finally to rhizosphere-mediated biochemical mobilization. To test this idea, we quantified fine-root morphology, absorptive-transport partitioning, anatomy, phosphatase activity, exudation, community-scale belowground structure, and soil and rhizosphere properties across woody communities representing approximately 20, 40, and 90 years since deglaciation in the Hailuogou Glacier foreland. Across succession stages, bulk density and pH declined, whereas field capacity, soil carbon, and soil nitrogen increased, indicating rapid development of the belowground resource environment. Fine-root strategies did not fall along a single acquisitive–conservative continuum. Instead, morphological nutrient capture peaked at intermediate succession: the 40-year stage had the highest specific root length, specific root area, absorptive-to-transport root length ratio, and root nitrogen concentration. In contrast, the 90-year stage showed lower specific root length but higher dry matter content, thicker cortex, greater standing fine-root biomass, larger rhizosphere volume, higher phosphatase activity, and greater area-based carbon exudation. This late-successional syndrome coincided with stronger extracellular enzyme activity, larger dissolved organic carbon and nitrogen pools, and higher microbial biomass, despite negative net nitrogen mineralization. Species-level analyses showed that biochemical-input traits were jointly shaped by successional stage, species identity, and their interaction. Together, these results show that primary succession did not simply increase or decrease root acquisitiveness. Instead, as soils developed, it changed the nutrient-acquisition pathway that dominated, with direct implications for nutrient cycling and vegetation dynamics in rapidly developing glacier-foreland ecosystems. Full article
(This article belongs to the Section Forest Soil)
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27 pages, 3100 KB  
Article
Comparative Ecological and Metagenomic Characterisation of Wild Legume Habitats in Bulgaria: Kaliakra, Strandzha, and Eastern Rhodopes
by Mariana Petkova, Nurettin Tahsin and Mariya Sabeva
Agronomy 2026, 16(9), 910; https://doi.org/10.3390/agronomy16090910 - 30 Apr 2026
Viewed by 219
Abstract
Wild relatives of cultivated legumes represent valuable genetic resources for crop improvement, ecosystem resilience, and sustainable agriculture. This study presents a comparative ecological and metagenomic assessment of three biogeographically distinct regions in Bulgaria—Kaliakra, Strandzha, and the Eastern Rhodopes—where populations of wild legumes, including [...] Read more.
Wild relatives of cultivated legumes represent valuable genetic resources for crop improvement, ecosystem resilience, and sustainable agriculture. This study presents a comparative ecological and metagenomic assessment of three biogeographically distinct regions in Bulgaria—Kaliakra, Strandzha, and the Eastern Rhodopes—where populations of wild legumes, including Pisum elatius, Cicer montbrettii, Vicia incisa, and Lupinus spp., occur. Field expeditions were conducted during flowering and seed maturation stages, followed by rhizosphere soil sampling and high-throughput sequencing targeting bacterial 16S rRNA and fungal ITS regions. Soil physicochemical properties, microbial diversity indices, and taxonomic composition were analysed and compared among regions. Distinct microbial community structures were identified. Kaliakra soils were dominated by Firmicutes (26–58%) and Proteobacteria (20–25%), while Strandzha soils showed higher abundance of Actinobacteriota (12–68%) and Proteobacteria (10–35%). The Eastern Rhodopes exhibited more balanced communities, with Proteobacteria (30–45%), Firmicutes (7–43%), and Actinobacteriota (3–11%). Fungal communities also differed significantly, with Nectriaceae dominating in Kaliakra, higher evenness in Strandzha, and intermediate diversity in the Eastern Rhodopes. Alpha diversity revealed the highest bacterial richness in Kaliakra, whereas the Eastern Rhodopes showed the greatest community evenness. Beta diversity analysis demonstrated clear regional separation driven by environmental filtering. These findings highlight the ecological and microbiological differentiation of wild legume habitats and support their conservation and utilisation in sustainable agriculture and breeding programs. Full article
(This article belongs to the Special Issue Recent Developments in Biological Nitrogen Fixation in Plants)
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25 pages, 3955 KB  
Article
Root Exudates Are Linked to Antibiotic Resistance Gene Variation by Modulating Rhizosphere Microbial Community Assembly Under Swine Wastewater Irrigation
by Liwei Liu, Meng Wang, Xiuzhi Wang, Yuan Liu and Zhongyang Li
Antibiotics 2026, 15(5), 444; https://doi.org/10.3390/antibiotics15050444 - 29 Apr 2026
Viewed by 350
Abstract
Background: Irrigation with swine wastewater may increase the dissemination risk of antibiotic resistance genes (ARGs) in the rhizosphere and alter root exudate composition. However, the relationship between root exudates and ARG dynamics under swine wastewater irrigation remains poorly understood. This study therefore [...] Read more.
Background: Irrigation with swine wastewater may increase the dissemination risk of antibiotic resistance genes (ARGs) in the rhizosphere and alter root exudate composition. However, the relationship between root exudates and ARG dynamics under swine wastewater irrigation remains poorly understood. This study therefore aimed to clarify how root exudates are connected with ARG dynamics under swine wastewater irrigation. Methods: To address this, untargeted metabolomics and metagenomic sequencing were combined to characterize rhizosphere ARG composition, microbial community structure, and root exudate profiles in different soybean cultivars under swine wastewater irrigation. Results: The results showed that irrigation water source and soybean cultivar were associated with variation in soil ARG composition and changes in plant root metabolic profiles. Under wastewater irrigation, the relative abundances of secondary metabolites in root exudates were generally elevated, particularly those of organic nitrogen compounds and organic oxygenated compounds. Cultivar-related variation remained evident in rhizosphere microbial communities and ARG profiles, and differences in exudate composition among cultivars became smaller. Irrigation water source and soybean cultivar were associated with changes in ARG dynamics. This association was mainly linked to variation in rhizosphere microbial community structure rather than direct effects of root exudates on ARGs. Xanthine and 3-isobutylpentanedioic acid, identified as key root exudates, increased under wastewater irrigation and were related to variation in the potential ARG host genus SCGC-AG-212-J23 and the related ARGs. In contrast, 5-methylheptan-3-one decreased under wastewater irrigation and was correlated with variation in SCGC-AG-212-J23, Gp6-AA40, and the related ARGs. Conclusions: Swine wastewater irrigation and soybean cultivar altered root metabolism, which were linked to variation in rhizosphere microbial communities. These changes may have collectively contributed to shifts in rhizosphere ARGs. This could provide a basis for understanding the ecological relationships among root exudates, microorganisms, and ARGs under swine wastewater irrigation. Full article
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23 pages, 3113 KB  
Article
Microhabitat Primarily Structures Bacterial Communities, While Management History Shapes Functional Potential in Tomato-Associated Soils
by Santiago Adolfo Vio, Joaquín Rilling, Manuel Fernandez-Lopez, Milko Alberto Jorquera, Mariano Pistorio and María Flavia Luna
Diversity 2026, 18(5), 256; https://doi.org/10.3390/d18050256 - 26 Apr 2026
Viewed by 352
Abstract
Intensive horticultural management modifies soil physicochemical conditions, yet its effects on microbial community assembly and functional organization remain poorly resolved. This study examined bulk soil (BS) and rhizosphere soil (Rh) bacterial communities associated with tomato plants grown in two contrasting commercial horticultural establishments: [...] Read more.
Intensive horticultural management modifies soil physicochemical conditions, yet its effects on microbial community assembly and functional organization remain poorly resolved. This study examined bulk soil (BS) and rhizosphere soil (Rh) bacterial communities associated with tomato plants grown in two contrasting commercial horticultural establishments: a long-term intensive monoculture (>10 years; MC) and a recently established system (FC). Total bacterial abundance and community structure were characterized using qPCR and 16S rRNA gene amplicon sequencing, respectively; the abundance and diversity of functional plant-growth-promoting (PGP) genes—nifH, phoD, and acdS—were assessed by qPCR and DGGE profiling. The MC system, associated with increased salinity, nutrient accumulation, and organic matter content, supported higher bacterial abundance, whereas the FC system showed a higher relative abundance of PGP genes. Amplicon sequencing revealed significant differentiation between BS and Rh, identifying microhabitat in tomato-associated soil as the primary driver of taxonomic structure, while site effects were weaker. In contrast, DGGE profiling supported differences in functional gene composition between management systems, whereas predicted pathway profiles inferred from 16S data were comparatively similar across samples. Overall, these results indicate that horticultural intensification is associated with shifts in predicted functional potential that are not paralleled by major changes in taxonomic structure. Full article
(This article belongs to the Special Issue Rhizosphere Microbial Community Diversity)
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10 pages, 2744 KB  
Proceeding Paper
Effects of Different Garlic Straw Additions on Eggplant Rhizosphere Matrix Microorganisms
by Xin Meng and Mengyi Wang
Biol. Life Sci. Forum 2025, 51(1), 16; https://doi.org/10.3390/blsf2025051016 - 23 Apr 2026
Viewed by 167
Abstract
Garlic has broad-spectrum antibacterial activity. Returning garlic straw to the field can promote crop growth and soil conditions to varying degrees. To explore the effects of different amounts of garlic straw added to the microorganisms in the rhizosphere substrate of eggplants, potted plant [...] Read more.
Garlic has broad-spectrum antibacterial activity. Returning garlic straw to the field can promote crop growth and soil conditions to varying degrees. To explore the effects of different amounts of garlic straw added to the microorganisms in the rhizosphere substrate of eggplants, potted plant experiments were carried out in the climate room of the East Campus of Tianjin Agricultural University. Three treatments were set up: T0 was eggplant single-cropping (CK), T1 was adding straw with fourteen garlic cloves planted in each pot (a total of 60.2 g), and T2 was adding straw with nine garlic bulbs planted in each pot, totalling 108 garlic cloves (a total of 463.5 g). Each treatment was repeated three times. The abundance of microbial species and the diversity of community structure in the rhizosphere matrix of eggplants were determined by high-throughput sequencing technology. The results indicated that adding garlic straw to the substrate could increase the dominant bacterial species in the microbial community structure of the eggplant rhizosphere substrate. The main bacterial phyla in the substrate were Proteobacteria, Chloroflexi, and Actinobacteriota. The genus of substrate bacteria is mainly Hirschia. The stromal fungi phylum is mainly composed of Ascomycota and Basidiomycota. In terms of Alpha diversity, the diversity and richness of bacteria and fungi in the rhizosphere matrix of eggplants have both decreased, indicating that garlic straw has shown good antibacterial properties, inhibiting the growth of certain pathogenic bacteria, reducing the occurrence of diseases, and improving the microbial environment. Therefore, garlic straw can improve the microbial environment of the rhizosphere substrate by increasing the dominant microbial community of the substrate and inhibiting the growth of pathogenic bacteria. This study provides a scientific basis and technical reference for choosing the appropriate way to add garlic straw and researching the microbial environment of the rhizosphere substrate of eggplants. Full article
(This article belongs to the Proceedings of The 9th International Horticulture Conference & Expo)
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Article
Plant-Derived Organic Acids Are Linked to Arbuscular Mycorrhizal Fungi and phoD-Harboring Bacteria Associated with Improved Soil Phosphorus Availability Across Plant Functional Groups in Karst Ecosystems
by Shu Zhang, Fujing Pan, Yueming Liang, Kelin Wang, Zijun Liu and Wei Zhang
Microorganisms 2026, 14(5), 952; https://doi.org/10.3390/microorganisms14050952 - 23 Apr 2026
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Abstract
Phosphorus (P) limitation is prevalent in terrestrial ecosystems. Plants can improve soil P availability through the exudation of organic acids and symbiotic interactions with microorganisms. However, associations between different plant functional groups and phosphorus cycling in P limited karst ecosystems remain poorly understood. [...] Read more.
Phosphorus (P) limitation is prevalent in terrestrial ecosystems. Plants can improve soil P availability through the exudation of organic acids and symbiotic interactions with microorganisms. However, associations between different plant functional groups and phosphorus cycling in P limited karst ecosystems remain poorly understood. To investigate this, the exudation rates of oxalic, citric and acetic acids from fine roots, the contents of carbon, nitrogen, and P in leaves and fine roots, and the contents of oxalic, citric and acetic acids, total P, available P (AP), and microbial biomass P in rhizosphere soils were measured across different plant functional groups in a karst ecosystem in southwestern China. Additionally, the activities of acid and alkaline phosphatases were also analyzed, as well as the relative abundance, community structure, diversity, and co-occurrence network patterns of arbuscular mycorrhizal fungi (AMF) and alkaline phosphatase-encoding (phoD) gene-harboring bacteria. The results showed that both the exudation rates and the contents of organic acids and AP were highest in the tree group, followed by the shrub and grass groups. The AP content of the legume group was significantly higher than that of the non-legume group. The exudation rates of oxalic acid were significantly greater than those of citric and acetic acids. AMF diversities were highest in the shrub and legume groups. The diversities of phoD-harboring bacteria decreased from the tree group to the shrub group and then to the grass group, yet there were no significant differences between the legume and non-legume groups. The communities of both AMF and phoD-harboring bacteria exhibited significant differences among these plant functional groups. The prevalent genera of phoD-harboring bacteria across all groups were Pseudomonas and Halomonas, with Halomonas being particularly prevalent in the legume group. The AMF community was dominated by Glomus, which attained its highest relative abundance in the tree and legume groups. Furthermore, the increased exudation rate and content of oxalic acid were associated with higher relative abundances of Glomus in AMF and Pseudomonas and Bacillus among phoD-harboring bacteria. Structural Equation Model (SEM) analysis demonstrated that plant-exuded organic acids, especially oxalic acid, were positively associated with P availability indirectly through their linkages with the diversity and abundance of AMF and phoD-harboring bacteria. The crucial role of oxalic acid was particularly prominent in the tree and legume groups. Our findings suggest that screening AMF and phoD-harboring bacteria with highly efficient P transformation activity and inoculating them into the rhizosphere of plants with high oxalic acid exudation could help improve plant resilience to P limitation and support sustainable restoration in karst ecosystems. Full article
(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling: 2nd Edition)
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