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Keywords = soil physicochemical analysis

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21 pages, 6874 KB  
Article
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
Viewed by 72
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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25 pages, 10585 KB  
Article
Spatiotemporal Patterns and Driving Mechanisms of Heavy Metal Accumulation in China’s Farmland Soils Based on Meta-Analysis and Machine Learning
by Jiamin Zhao, Rui Guo, Junkang Guo, Zihan Yu, Jingwen Xu, Xiaoyan Zhang and Liying Yang
Sustainability 2025, 17(24), 11318; https://doi.org/10.3390/su172411318 - 17 Dec 2025
Viewed by 91
Abstract
To elucidate the long-term spatiotemporal patterns and key drivers factors, this study employed a meta-analysis of data from soil containing Potentially Toxic Elements (Cd, As, Cr, Hg, and Pb) in Chinese farmland soils from 2003 to 2025. The geoaccumulation index, the potential ecological [...] Read more.
To elucidate the long-term spatiotemporal patterns and key drivers factors, this study employed a meta-analysis of data from soil containing Potentially Toxic Elements (Cd, As, Cr, Hg, and Pb) in Chinese farmland soils from 2003 to 2025. The geoaccumulation index, the potential ecological risk index, and standard deviation ellipses were used to assess the spatiotemporal evolution of heavy metal accumulation and ecological risk, while the Random forest–SHapley Additive exPlanations (RF-SHAP) method was employed to identify driving mechanisms. At the national scale, Cd and Hg are significantly enriched relative to the background values, whereas As, Cr, and Pb remained at relatively low levels, with enrichment ranked as Cd > Hg > Pb > Cr > As. Cd and Hg indicated mild pollution, but the Sichuan Basin emerged as a hotspot, where Cd reached moderate pollution and showed strong ecological risk, and Hg also exhibited high ecological risk. Over the past two decades, the contamination center shifted from coastal to southwestern inland regions, with an expanded and more dispersed distribution. Since 2017, Cd and Hg pollution levels have stabilized, suggesting that the aggravating trend has been preliminarily curbed. Industrial waste and wastewater discharge, irrigation and fertilization were identified as the primary anthropogenic factors of soil heavy metal accumulation, while climatic factors (temperature, precipitation, and solar radiation) and soil physicochemical properties (pH, clay content, and organic matter) played fundamental roles in spatial distribution and accumulation. Our findings call for targeted predictive research and policies to manage heavy metal risks and preserve farmland sustainability in a changing climate. Full article
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17 pages, 3264 KB  
Article
Effects of Invasive Solidago canadensis and Biochar on the Remediation of Soil Cd Contamination and Greenhouse Gas Emissions
by Xiaokang Ni, Yadi Yu, Xi Liu, Wanqing Nie, Yuli Hu, Jian Bai, Ziyi Yan, Wei Li, Lifei Xiong, Xixian Xie, Yuanyuan Zhu, Zihan Zeng, Qingye Yu, Shuli Wang, Qin Ying, Nansheng Wu and Ling Zhang
Life 2025, 15(12), 1927; https://doi.org/10.3390/life15121927 - 16 Dec 2025
Viewed by 111
Abstract
Cadmium (Cd) contamination in agricultural soils threatens food security and exacerbates climate change through its impact on greenhouse gas (GHG) (CO2, N2O and CH4) emissions, in which N2O and CO2 are the dominant fluxes [...] Read more.
Cadmium (Cd) contamination in agricultural soils threatens food security and exacerbates climate change through its impact on greenhouse gas (GHG) (CO2, N2O and CH4) emissions, in which N2O and CO2 are the dominant fluxes of the terrestrial carbon-nitrogen cycle whose magnitude is directly amplified by Cd stress. Key remediation approaches for this dual challenge are phytoremediation and biochar amendment. This study aims to investigate the effects of Solidago canadensis (CGR) and biochar (BC) on soil remediation and GHG emissions under different levels of Cd contamination. A pot experiment with four Cd concentration gradients (0, 5, 10, and 30 mg kg−1, i.e., Cd-0, Cd-5, Cd-10, and Cd-30, respectively) and three remediation measures (control, BC addition, and CGR cultivation) was set up to measure available soil Cd (ACd), soil physicochemical properties, GHG emissions, and plant Cd accumulations. The results demonstrated that ACd was significantly reduced by BC via adsorption through surface complexation and by CGR via immobilization through root uptake and sequestration. CGR decreased ACd by 46.2% and 41.7% under mild and moderate Cd contamination, respectively, while BC reduced ACd by 8.9% under severe contamination. In terms of GHG emissions, CGR increased cumulative CO2 by 83.4% in Cd-10 soil and 53.8% in Cd-30 soil, whereas BC significantly lowered N2O emissions by 22.1% in Cd-5 soil. Mantel analysis revealed strong correlations between ACd and key carbon and nitrogen indicators, which mediate the bioavailability of Cd. Therefore, CGR cultivation is better suited to mild-to-moderate contamination given its high removal efficiency, while BC amendment is targeted at severe contamination by stabilizing Cd and mitigating N2O. This provides a scientific basis for the remediation of Cd-contaminated soils. Full article
(This article belongs to the Section Plant Science)
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21 pages, 4632 KB  
Article
Environmental and Rhizosphere Microbiome Drivers of Metabolic Profiles in Gastrodia elata: An Integrative Analysis of Soil, Metabolomics and Anti-Inflammatory Readouts
by Yan Yang, Longxing Guo, Yongguo Li, Miaomiao Ji, Tingting He, Kaiming Hou, Jian Li, Haonan Zhang, Zhilong Shi and Haizhu Zhang
Foods 2025, 14(24), 4265; https://doi.org/10.3390/foods14244265 - 11 Dec 2025
Viewed by 296
Abstract
Background: Gastrodiae Rhizoma, the dried tuber of Gastrodia elata Bl. (Orchidaceae), is a traditional Chinese medicinal (TCM) and edible plant. Its quality formation is closely associated with rhizosphere microorganisms; however, the specific underlying mechanisms remain unclear. Methods: Tubers and rhizosphere soils were collected [...] Read more.
Background: Gastrodiae Rhizoma, the dried tuber of Gastrodia elata Bl. (Orchidaceae), is a traditional Chinese medicinal (TCM) and edible plant. Its quality formation is closely associated with rhizosphere microorganisms; however, the specific underlying mechanisms remain unclear. Methods: Tubers and rhizosphere soils were collected from seven major production regions of G. elata. Soil physicochemical properties were analyzed, and integrative analyses combining soil microbiome and untargeted metabolome profiling were conducted. The anti-inflammatory activity of G. elata extracts was evaluated using a RAW264.7 macrophage model. Multivariate statistical approaches, including OPLS-DA and correlation network analysis, were used to decipher relationships among environmental factors, microbial communities, metabolic profiles, and bioactivities. Results: A total of 39,250 bacterial ASVs and 10,544 fungal ASVs were identified. The bacterial community, dominated by Proteobacteria and Acidobacteria, was strongly influenced by soil chemical factors, including pH and total nitrogen. The fungal community, primarily composed of Ascomycota and Basidiomycota, exhibited marked sensitivity to altitudinal gradients. Correlation analysis revealed that key secondary metabolites, including flavonoids and phenolic acids, along with their anti-inflammatory activities, were significantly associated with rhizosphere microorganisms such as Edaphobaculum, Hypocrea, and Pseudomonas. Conclusions: Our findings outline the pathways connecting environmental factors, the microbiome, and functional metabolites in G. elata, highlighting the importance of environmental–microbial interactions in determining metabolic outcomes. This work provides new insights into the ecological and molecular mechanisms behind the quality formation of this medicinal plant. Full article
(This article belongs to the Section Food Nutrition)
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17 pages, 3832 KB  
Article
Growth and Habitat Adaptability of Madhuca hainanensis Under Different Elevation and Canopy Closure Conditions
by Ru Wang, Xiaoyan Wang, Bijia Zhang, Liguo Liao, Jia Yang, Xin Li, Zuojun Duan, Fangneng Lin, Biao Wu, Shiqi Huang and Jinrui Lei
Forests 2025, 16(12), 1844; https://doi.org/10.3390/f16121844 - 10 Dec 2025
Viewed by 135
Abstract
Madhuca hainanensis is a rare, endemic tree species of Hainan Island, with considerable ecological and economic value. Its natural regeneration is severely limited by habitat fragmentation and environmental stress. To investigate its adaptive across environmental gradients, we established experimental plots in the Jianfengling [...] Read more.
Madhuca hainanensis is a rare, endemic tree species of Hainan Island, with considerable ecological and economic value. Its natural regeneration is severely limited by habitat fragmentation and environmental stress. To investigate its adaptive across environmental gradients, we established experimental plots in the Jianfengling area of Hainan Tropical Rainforest National Park, encompassing elevation (400–1000 m) and canopy closure (30%–90%) gradients. Sapling growth and health were monitored for one year, alongside measurements of soil physicochemical properties and leaf photosynthetic pigment content. The results indicate that elevation was the primary factor influencing growth, with saplings at lower elevations exhibiting higher increments in height, diameter, and crown spread. While canopy closure was not statistically significant, moderate openness (30%–50%) at low elevations favored growth, whereas high-elevation, heavily shaded conditions constrained development. Sapling health declined over time, particularly in high-elevation and high-canopy-closure plots, and the interaction between elevation and canopy closure amplified physiological stress. Redundancy analysis revealed that elevation and canopy closure jointly explained ~36%–38% of the variance in growth and health, with chlorophyll a, carotenoids, and soil available phosphorus also contributing to sapling performance. These findings indicate that M. hainanensis is highly sensitive to light and elevation-related environmental gradients, and that low-elevation sites with moderate canopy openness are optimal for restoration and cultivation. This study provides a scientific basis for in situ conservation, wild reintroduction, and management of this threatened endemic species. Full article
(This article belongs to the Section Forest Ecophysiology and Biology)
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17 pages, 2571 KB  
Article
Foliar Fertilization-Induced Rhizosphere Microbial Mechanisms for Soil Health Enhancement
by Qinwen Zeng, Hua Xie, Siyuan Zheng, Yuzhuo Zhao, Xiaoyue Zhang, Yunyou Zheng, Luotian Lu, Yonghong Liu, Fenghua Ding, Chengsen Zhao, Xinwei Song and Bin Ma
Agronomy 2025, 15(12), 2837; https://doi.org/10.3390/agronomy15122837 - 10 Dec 2025
Viewed by 207
Abstract
Foliar fertilization can influence soil health by altering soil physicochemical properties and nutrient cycling processes; however, its underlying mechanisms remain insufficiently understood. Here, we compared soils under two treatments—foliar fertilizer application (YMF) and no foliar fertilizer (CK)—and elucidated their effects on paddy soil [...] Read more.
Foliar fertilization can influence soil health by altering soil physicochemical properties and nutrient cycling processes; however, its underlying mechanisms remain insufficiently understood. Here, we compared soils under two treatments—foliar fertilizer application (YMF) and no foliar fertilizer (CK)—and elucidated their effects on paddy soil health and associated microbial mechanisms. Comprehensive analyses of soil physicochemical properties, microbial diversity, and functional gene profiles were also conducted. We found that foliar fertilization enhanced soil physicochemical and biological properties, particularly pH, CEC, SOM, TN, AP, and MBC, resulting in an increase in the soil health index (SHI) from 0.805 to 0.906. Metagenomic analysis further revealed that foliar fertilization enriched functional microbial taxa such as Actinomycetes, Defluviilinea, Roseovarius, and Bradyrhizobium, which enhanced the activities of key nutrient cycling pathways, including carbon stabilization (K14469, MDH sdhB), nitrogen metabolism (narY, nxrA, hdh), and phosphorus mineralization (htxA, phnH). These findings provide mechanistic insights into the microbial processes underlying foliar fertilizer–induced improvement in soil health and offer theoretical support for the development of precision fertilization and sustainable soil health management strategies in agricultural systems. Full article
(This article belongs to the Section Soil and Plant Nutrition)
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25 pages, 14917 KB  
Article
Medicinal Plant Rhizospheres as Reservoirs of Aspergillus-Derived Phytochemicals with Antimicrobial and Insecticidal Potential
by Sidra Farooq, Asif Mehmood, Nasir Ali, Amjad Khan and Naeem Khan
Life 2025, 15(12), 1886; https://doi.org/10.3390/life15121886 - 10 Dec 2025
Viewed by 180
Abstract
The rhizosphere, a dynamic interface shaped by plant root exudates, fosters microbial communities with significant biochemical potential. This study investigated the interplay between soil properties and fungal bioactivity in the rhizospheres of Withania coagulans and Justicia adhatoda in Pakistan. Physicochemical analysis revealed silty [...] Read more.
The rhizosphere, a dynamic interface shaped by plant root exudates, fosters microbial communities with significant biochemical potential. This study investigated the interplay between soil properties and fungal bioactivity in the rhizospheres of Withania coagulans and Justicia adhatoda in Pakistan. Physicochemical analysis revealed silty loam textures with divergent phosphorus [25.7 vs. 71.5 mg/kg] and potassium [108 vs. 78 mg/kg] levels, alongside near-neutral pH, influencing microbial dynamics. Two fungal isolates, Aspergillus luchuensis and A. flavus, were identified through morphological traits and ITS-region sequencing. Gas chromatography-mass spectrometry [GC-MS] profiling of ethyl acetate extracts uncovered 30 and 25 previously uncharacterized metabolites in A. luchuensis and A. flavus, respectively, including bioactive compounds such as tetradecanoic acid and nonadecane. Bioassays demonstrated broad-spectrum efficacy against multidrug-resistant clinical isolates, with A. flavus exhibiting notable inhibition against Salmonella typhi [31.7 mm zone] and A. luchuensis against Shigella spp. [23 mm]. Both extracts suppressed Lemna minor growth by 70%, indicating phytotoxic potential, and displayed species-specific insecticidal activity, inducing 70% mortality by A. luchuensis against Blattodea and 50% by A. flavus against the same species. These findings underscore the rhizosphere’s role as a reservoir of bioactive fungi, with Aspergillus spp. producing metabolites of pharmaceutical and agrochemical relevance. The study highlights the necessity for advanced structural elucidation and ecotoxicological assessments to harness these compounds, advocating integrated approaches combining metabolomics and genomic mining to unlock novel biotechnological applications. Full article
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15 pages, 1432 KB  
Article
Topographic and Edaphic Drivers of Community Structure and Species Diversity in a Subtropical Deciduous Broad-Leaved Forest in Eastern China
by Zeyu Xiang, Jingxuan Wang, Dan Xi, Zhaochen Zhang, Zhongbing Tang, Yunan Hu, Jiaxin Zhang and Saixia Zhou
Forests 2025, 16(12), 1837; https://doi.org/10.3390/f16121837 - 10 Dec 2025
Viewed by 135
Abstract
Subtropical deciduous broad-leaved forests in eastern China form a key ecotone between temperate and subtropical biomes, yet their vegetation–environment relationships remain insufficiently understood. This study examined community structure, species diversity, and their associations with topographic and soil variables in a 25 ha forest [...] Read more.
Subtropical deciduous broad-leaved forests in eastern China form a key ecotone between temperate and subtropical biomes, yet their vegetation–environment relationships remain insufficiently understood. This study examined community structure, species diversity, and their associations with topographic and soil variables in a 25 ha forest dynamics plot in the Lushan Mountains. All woody plants with a diameter at breast height (DBH) ≥ 1 cm were surveyed, and detailed topographic attributes and soil physicochemical properties were measured. Community structure showed strong linkages with species diversity: tree-layer structural characteristics were generally negatively correlated with diversity, whereas in the shrub layer, density was negatively but height and DBH were positively correlated with diversity. Species diversity in the two layers was positively associated, while tree-layer structure was negatively related to shrub-layer diversity. Among topographic factors, altitude and the topographic solar radiation aspect index (TRASP) exerted the strongest influences on soil properties, with altitude negatively correlated with soil pH and available nutrients but positively correlated with C:N, C:P, and total carbon, and TRASP showing negative correlations with most nutrients except total phosphorus. Redundancy analysis revealed that topographic heterogeneity and soil conditions jointly shaped community structure and species diversity, with soil C:N ratio, altitude, pH, total phosphorus, and total carbon emerging as key drivers. These findings demonstrate that areas with high plant diversity do not always correspond to high soil nutrient content and underscore the importance of integrating both topographic and edaphic factors into biodiversity conservation and forest management in subtropical deciduous broad-leaved forests. Full article
(This article belongs to the Section Forest Biodiversity)
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23 pages, 3382 KB  
Article
Optimizing Ridge–Furrow Configuration and Nitrogen Rate to Enhance Wheat Nitrogen Use Efficiency Under Diverse Climate and Soil Conditions
by Ting Pan, Zeyu Liu, Liuyang Yan, Fu Chen, Juanling Wang, Xuefang Huang and Yueyue Xu
Agriculture 2025, 15(24), 2543; https://doi.org/10.3390/agriculture15242543 - 8 Dec 2025
Viewed by 250
Abstract
Optimizing field cropping practices to improve nitrogen use efficiency is imperative to promote intensive and sustainable wheat production. As a cultivation method commonly adopted in arid and semi-arid regions globally, the ridge–furrow mulching system (RFMS) is capable of efficiently harvesting rainfall, reduce evaporation [...] Read more.
Optimizing field cropping practices to improve nitrogen use efficiency is imperative to promote intensive and sustainable wheat production. As a cultivation method commonly adopted in arid and semi-arid regions globally, the ridge–furrow mulching system (RFMS) is capable of efficiently harvesting rainfall, reduce evaporation losses, enhancing soil moisture levels in the root zone, and boosting crop productivity. However, the combined effects of varying ridge–furrow ratios (RD), ridge heights (RH), and nitrogen application rates (RN) on nitrogen fertilizer bias productivity (PFPN) under the influence of climatic conditions, soil types, and field management practices remain poorly understood due to a lack of systematic evaluation. This study conducted a meta-analysis of 462 comparative datasets from 98 research projects to reveal the interactive effects of RFMS and nitrogen fertilizer across climatic gradients. The results showed that RH, RD, and RN increased by 23.78%, 22.37%, and 23.07% respectively (p < 0.05), with the most significant enhancement of PFPN being demonstrated by RH. The most significant improvement in PFPN was observed when RD = 1:1, R < 10 cm, and RN > 200 kg∙hm−2, with PFPN increasing by 27.7%, 29.50%, and 29.32% respectively (p < 0.05). Climatic and soil physico-chemical factors and field management practices are the key factors influencing the RFMS. When average annual evapotranspiration (AE) < 1000, RN > 200 has the best effect on nitrogen utilization efficiency, while under the condition of AE > 1500, RN < 100 is more effective. In terms of mulching strategy, full mulching of ridges and furrows is recommended in areas with severe drought and low temperatures, while mulching only ridges or furrows is more appropriate in areas with relatively mild climate. The present study provides a scientific basis for the optimal design of ridge–furrow mulching configuration and nitrogen application level. This is achieved by considering climatic conditions, soil fertility, and field management in agro-ecosystems in arid and semi-arid areas. Full article
(This article belongs to the Section Agricultural Soils)
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20 pages, 5164 KB  
Article
Stand Density Drives Soil Microbial Community Structure in Response to Nutrient Availability in Larix gmelinii var. principis-rupprechtii (Mayr) Pilger Plantations
by Fengzi Li, Lei Liu, Long Hai, Hongwei Yang, Kai Zhao, Qiuming Di and Zhibo Wang
Plants 2025, 14(24), 3737; https://doi.org/10.3390/plants14243737 - 8 Dec 2025
Viewed by 258
Abstract
Sustainable forest management requires a comprehensive understanding of how stand density regulates soil ecological processes. We examined a Larix principis-rupprechtii plantation under three thinning retention densities (High—HD; Medium—MD; Low—LD) and an unthinned control (CK), with soil samples collected from four depth layers (0–10, [...] Read more.
Sustainable forest management requires a comprehensive understanding of how stand density regulates soil ecological processes. We examined a Larix principis-rupprechtii plantation under three thinning retention densities (High—HD; Medium—MD; Low—LD) and an unthinned control (CK), with soil samples collected from four depth layers (0–10, 10–20, 20–30, and 30–40 cm). This study investigated the effects of stand density on soil properties and microbial communities in a Larix principis-rupprechtii plantation by combining high-throughput sequencing with soil physicochemical analysis to identify the optimal density regime for maintaining soil health. Results demonstrated the following: (1) Moderate-density (MD) management best balanced the stability of soil ecosystem structure, showing superior water retention, organic carbon content, and microbial diversity in the 0–30 cm soil layer. The mechanism underlying these improvements can be attributed to the moderately open canopy structure in MD stands, which facilitated efficient litter decomposition and drove functional complementarity between Basidiomycota (enhancing cellulose degradation capacity) and Acidobacteriota (adapted to oligotrophic conditions). (2) Redundancy analysis revealed that soil pH and available nutrients (AK, AP) were key environmental factors driving microbial community restructuring: Actinobacteriota dominated in neutral, phosphorus-rich environments, while Acidobacteriota thrived under acidic, phosphorus-limited conditions. Fungal communities showed high sensitivity to management intensity, with significant shifts between Ascomycota and Basidiomycota, whereas bacterial communities remained relatively stable due to functional redundancy. We recommend the adoption of moderate-density management as a sustainable practice to enhance soil nutrient cycling and maintain microbial diversity, thereby providing scientific support for sustainable plantation management. Full article
(This article belongs to the Section Plant–Soil Interactions)
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19 pages, 2350 KB  
Article
Differential Assembly of Rhizosphere Microbiome and Metabolome in Rice with Contrasting Resistance to Blast Disease
by Jian Wang, Deqiang Li, Daihua Lu, Cheng Chen, Qin Zhang, Rongtao Fu and Fu Huang
Microorganisms 2025, 13(12), 2789; https://doi.org/10.3390/microorganisms13122789 - 8 Dec 2025
Viewed by 199
Abstract
Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases threatening global rice production. Although host resistance represents a sustainable control strategy, the underlying mechanisms mediated by the rhizosphere microbiome remain poorly understood. In this study, we selected four [...] Read more.
Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases threatening global rice production. Although host resistance represents a sustainable control strategy, the underlying mechanisms mediated by the rhizosphere microbiome remain poorly understood. In this study, we selected four rice varieties with varying resistance to blast and demonstrated, through an integrated approach of 16S rRNA/ITS amplicon sequencing, untargeted metabolomics, and soil physicochemical analysis, that the rice genotype reprograms the genotype-root exudate-rhizosphere microbiome system. Results showed that the resistant variety P104 significantly decreased the soil pH while increasing the contents of total nitrogen, ammonium nitrogen, and nitrate nitrogen. On the other hand, the susceptible variety P302 exhibited higher pH and available phosphorus content. Furthermore, the rhizosphere of P104 was enriched with specific beneficial microbes such as Desulfobacterota, Ascomycota, and Pseudeurotium, and activated defense-related metabolic pathways including cysteine and methionine metabolism and phenylpropanoid biosynthesis. In contrast, susceptible varieties showed reduced bacterial diversity and fostered a microecological environment more conducive to pathogen proliferation. Our findings indicate that blast-resistant rice genotypes are associated with a protective rhizosphere microbiome, potentially mediated by alterations in root metabolism, thereby suppressing pathogen establishment. These insights elucidate the underground mechanisms of blast resistance and highlight the potential of microbiome-assisted breeding for sustainable crop protection. Full article
(This article belongs to the Section Plant Microbe Interactions)
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19 pages, 8957 KB  
Article
Mean Annual Temperature, Soil Organic Matter and Phyllospheric Bacterial Diversity Shape Biomass of Dominant Species Along a Degradation Gradient in Alpine Steppes: A Case Study from the Qinghai–Tibet Plateau
by Kaifu Zheng, Xin Jin, Jingjing Li and Guangxin Lu
Microorganisms 2025, 13(12), 2787; https://doi.org/10.3390/microorganisms13122787 - 7 Dec 2025
Viewed by 273
Abstract
The structure and function of alpine steppes are maintained largely by dominant species, which in turn determine the productivity and stability of plant communities. Nutrient acquisition and stress regulation may, to some extent, be mediated by phyllospheric microbiota at the interface of plants [...] Read more.
The structure and function of alpine steppes are maintained largely by dominant species, which in turn determine the productivity and stability of plant communities. Nutrient acquisition and stress regulation may, to some extent, be mediated by phyllospheric microbiota at the interface of plants with the atmosphere, and phyllospheric microbes are capable of amplifying and transmitting vegetation responses to degradation. Previous research has mainly addressed climate, soil, vegetation and soil microbiota or has assessed phyllosphere communities as a whole, thereby overlooking the specific responses of phyllospheric bacteria associated with the vegetation-dominant species Stipa purpurea along gradients of vegetation degradation in alpine steppes. In this study, we characterised vegetation degradation at the community level (from non-degraded to severely degraded grasslands) and quantified associated changes in the dominant species Stipa purpurea (cover, height and aboveground biomass) and its phyllospheric bacterial communities, in order to elucidate response patterns within the coupled system of host plants, phyllosphere microbiota, climate (mean annual temperature and precipitation) and soil physicochemical properties. Compared with non-degraded (ND) grasslands, degraded sites had a 22.6% lower mean annual temperature (MAT) and reductions in total nitrogen, nitrate nitrogen, organic matter (OM) and soil quality index (SQI) of 49.4%, 55.6%, 46.8% and 47.6%, respectively. Plant community cover and the aboveground biomass of dominant species declined significantly with increasing degradation. Along the vegetation-degradation gradient from non-degraded to severely degraded alpine steppes, microbial source-tracking analysis of the phyllosphere of the dominant species Stipa purpurea revealed a sharp decline in the contribution of phyllospheric bacterial sources. Estimated contributions from non-degraded sites to lightly, moderately and severely degraded sites were 95.68%, 62.21% and 6.89%, respectively, whereas contributions from lightly to moderately degraded and from moderately to severely degraded sites were 34.89% and 16.47%, respectively. Bacterial richness increased significantly, and β diversity diverged under severe degradation (PERMANOVA, F = 5.48, p < 0.01). From light to moderate degradation, biomass and relative cover of the dominant species decreased significantly, while the phyllosphere bacterial community appeared more strongly influenced by the host than by environmental deterioration; the community microbial turnover index (CMTB) and microbial resistance potential increased slightly but non-significantly (p > 0.05). Under severe degradation, worsening soil conditions and hydrothermal regimes exerted a stronger influence than the host, and CMTB and microbial resistance potential decreased by 6.5% and 34.1%, respectively (p < 0.05). Random-forest analysis indicated that climate, soil, phyllosphere diversity and microbial resistance jointly accounted for 42.1% of the variation in constructive-species biomass (R2 = 0.42, p < 0.01), with the remaining variation likely driven by unmeasured biotic and abiotic factors. Soil contributed the most (21.73%), followed by phyllosphere diversity (9.87%) and climate (8.62%), whereas microbial resistance had a minor effect (1.86%). Specifically, soil organic matter (OM) was positively correlated with biomass, whereas richness, beta diversity and MAT were negatively correlated (p < 0.05). Taken together, our results suggest that under ongoing warming on the Qinghai–Tibet Plateau, management of alpine steppes should prioritise grasslands in the early stages of degradation. In these systems, higher soil organic matter is associated with greater phyllospheric microbial resistance potential and increased biomass of Stipa purpurea, which may help stabilise this dominant species and slow further vegetation degradation. Full article
(This article belongs to the Section Environmental Microbiology)
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20 pages, 2923 KB  
Article
Different Land Use Patterns in Semi-Arid Regions Affect N2O Emissions by Regulating Soil Nitrification Functional Genes
by Jun Du, Mengyin Du, Yao Yao, Wanting Li, Guorong Xu, Weiwei Ma, Jianyu Yuan and Guang Li
Agronomy 2025, 15(12), 2810; https://doi.org/10.3390/agronomy15122810 - 6 Dec 2025
Viewed by 275
Abstract
Nitrous oxide (N2O), as one of the important greenhouse gases in the atmosphere, has a significant impact on global climate change. Its emissions are significantly regulated by land use changes, especially in ecologically fragile semi-arid areas. However, there is still a [...] Read more.
Nitrous oxide (N2O), as one of the important greenhouse gases in the atmosphere, has a significant impact on global climate change. Its emissions are significantly regulated by land use changes, especially in ecologically fragile semi-arid areas. However, there is still a lack of systematic analysis on the key biotic and abiotic factors through which different land use patterns affect N2O emissions. Therefore, this study focuses on four typical land use types in the Loess Plateau of central Gansu: Picea asperata (PA), Medicago sativa (MS), Abandoned land (AL), and Wheat field (WF). Static box gas chromatography was used to monitor soil N2O flux in situ, and multidimensional analysis was conducted based on soil physicochemical properties, microbial community structure, and nitrogen cycling functional genes. Based on the observational data from the 2024 growing season (April to October), Research findings show that the cumulative emissions of N2O from wheat fields increased significantly by 26.4%, 19.4%, and 39.8% compared to medicago sativa, abandoned land, and picea asperata, respectively. Mechanism analysis reveals that picea asperata promote nitrogen fixation and absorption in soil through higher soil water content and organic carbon content, as well as enrichment of Proteobacteria and high expression of nrfA and napA genes, thereby inhibiting N2O production and emissions. The wheat fields, on the other hand, have significantly increased N2O emissions due to the increased abundance of amoA_B, nxrB, and nirK functional genes and enhanced urease activity, which promote nitrification and denitrification processes. The Partial Least Squares Path Model (PLS-PM) further confirmed that nitrification functional genes are key driving factors for N2O emissions. This study systematically reveals the microbial and biochemical pathways involved in regulating N2O emissions through land use in semi-arid regions, providing a theoretical basis for regional nitrogen cycle management and climate mitigation. Full article
(This article belongs to the Section Agroecology Innovation: Achieving System Resilience)
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16 pages, 1183 KB  
Article
Effects of Long-Term Elevated CO2 on Soil Aggregate Structure and Microbial Communities in a Deyeuxia angustifolia Wetland of the Sanjiang Plain
by Lanying Shi, Hongjie Cao, Rongtao Zhang, Haixiu Zhong, Yingnan Liu, Jifeng Wang, Donglai Zhang, Lin Li and Hongwei Ni
Microorganisms 2025, 13(12), 2776; https://doi.org/10.3390/microorganisms13122776 - 5 Dec 2025
Viewed by 209
Abstract
To investigate the effects of long-term elevated atmospheric CO2 (eCO2) on the distribution and stability of soil aggregates and microbial characteristics in wetland soils and to reveal the mechanisms by which eCO2 influences soil organic carbon (SOC) sequestration, a [...] Read more.
To investigate the effects of long-term elevated atmospheric CO2 (eCO2) on the distribution and stability of soil aggregates and microbial characteristics in wetland soils and to reveal the mechanisms by which eCO2 influences soil organic carbon (SOC) sequestration, a multi-temporal-scale eCO2 control experiment was conducted in the Sanjiang Plain wetland with treatments at ambient CO2 concentration (AC), 550 ppm, and 700 ppm CO2. Soil aggregate fractionation, phospholipid fatty acid (PLFA) analysis, and redundancy analysis (RDA) were used to analyze changes in aggregate size distribution, stability indices (MWD, GMD), microbial biomass, and community structure. The results showed that eCO2 significantly affected aggregate size distribution. Both short- and long-term exposure to low-concentration eCO2 reduced the proportion of large aggregates. Over time, the proportion of silt and clay particles increased, while microaggregates decreased. Although CO2 concentration did not directly affect MWD and GMD, long-term eCO2 significantly reduced soil aggregate stability. Microbial biomass and diversity were not sensitive to CO2 concentration but decreased significantly with prolonged exposure. In contrast, microbial community structure was significantly affected by both CO2 level and exposure duration. RDA indicated that, under short-term eCO2, aggregate fractions were positively correlated with microbial biomass, whereas, under medium- and long-term treatments, they were positively correlated with soil physicochemical properties. Macroaggregates were positively correlated with aggregate stability, while microaggregates and silt–clay fractions were negatively correlated—a relationship that strengthened with longer eCO2 exposure. Thus, long-term eCO2 altered soil aggregate structure and microbial communities, ultimately influencing SOC stability. These findings provide data and theoretical support for predicting soil carbon stability and ecosystem functioning in wetlands under climate change. Full article
(This article belongs to the Section Environmental Microbiology)
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22 pages, 2659 KB  
Article
Biochar–Urea Peroxide Composite Particles Alleviate Phenolic Acid Stress in Pogostemon cablin Through Soil Microenvironment Modification
by Yuting Tu, Baozhu Chen, Qiufang Wei, Yanggui Xu, Yiping Peng, Zhuxian Li, Jianyi Liang, Lifang Zhuo, Wenliang Zhong and Jichuan Huang
Microorganisms 2025, 13(12), 2772; https://doi.org/10.3390/microorganisms13122772 - 5 Dec 2025
Viewed by 317
Abstract
The continuous-cropping obstacles of Pogostemon cablin (patchouli) is severely constrained by autotoxic phenolic acids accumulated in the rhizosphere soil. Biochar adsorption and chemical oxidation are common remediation strategies; they often fail to simultaneously and efficiently remove phenolic allelochemicals while improving the soil micro-ecological [...] Read more.
The continuous-cropping obstacles of Pogostemon cablin (patchouli) is severely constrained by autotoxic phenolic acids accumulated in the rhizosphere soil. Biochar adsorption and chemical oxidation are common remediation strategies; they often fail to simultaneously and efficiently remove phenolic allelochemicals while improving the soil micro-ecological environment. To address this issue, this study developed a novel biochar–urea peroxide composite particle (BC-UP). Batch degradation experiments and electron paramagnetic resonance (EPR) analysis confirmed the synergistic adsorption-oxidation function of BC-UP. A pot experiment demonstrated that application of BC-UP (5.0 g/kg) significantly alleviated phenolic acid stress. Specifically, BC-UP application significantly enhanced shoot biomass by 28.8% and root surface area by 49.3% compared to the phenolic acid-stressed treatment and concurrently reduced the total phenolic acid content in the rhizosphere soil by 37.3%. This growth promotion was accompanied by the enhanced accumulation of key bioactive compounds (volatile oils, pogostone, and patchouli alcohol). BC-UP amendment also improved key soil physicochemical properties (e.g., pH, and organic matter) and enhanced the activities of critical enzymes. Furthermore, BC-UP reshaped the microbial community, notably reducing the fungi-to-bacteria OTU ratio by 49.7% and enriching the relative abundance of Firmicutes and Nitrospirota but suppressing the Ascomycota phylum abundance. Redundancy analysis identified soil sucrase and catalase activity, total phenolic acid content, and Ascomycota abundance as key factors influencing patchouli biomass. In conclusion, BC-UP effectively mitigates phenolic acid stress through combined adsorption and radical oxidation, subsequently improving soil properties and restructuring the rhizosphere microbiome, offering a promising soil remediation strategy for patchouli and other medicinal crops. Full article
(This article belongs to the Topic Recent Advances in Soil Health Management)
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