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Search Results (2,053)

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Keywords = soil physicochemical

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18 pages, 2357 KiB  
Article
Nitrogen Fertilizer Reduction in Rice–Eel Co-Culture System Improves the Soil Microbial Diversity and Its Functional Stability
by Mengqian Ma, Weiguang Lv, Yu Huang, Juanqin Zhang, Shuangxi Li, Naling Bai, Haiyun Zhang, Xianpu Zhu, Chenglong Xu and Hanlin Zhang
Plants 2025, 14(15), 2425; https://doi.org/10.3390/plants14152425 - 5 Aug 2025
Abstract
The ecological rice–eel co-culture system is not only beneficial for enhancing productivity and sustainability in agriculture but also plays a crucial role in promoting environmental health. In the present study, based on the long-term positioning trial of the rice–eel co-culture system that began [...] Read more.
The ecological rice–eel co-culture system is not only beneficial for enhancing productivity and sustainability in agriculture but also plays a crucial role in promoting environmental health. In the present study, based on the long-term positioning trial of the rice–eel co-culture system that began in 2016 and was sampled in 2023, the effects of reduced nitrogen fertilizer application on soil physico-chemical properties and the bacterial community were investigated. Treatments included a conventional regular fertilization treatment (RT), rice–eel co-culture system regular fertilization (IT), and nitrogen-reduction 10%, 30%, and 50% fertilization treatments (IT90, IT70, and IT50). Our research demonstrated the following: (1) Compared to RT, IT significantly increased soil water-stable macroaggregates (R0.25), mean weight diameter (MWD), geometric mean diameter (GMD), and available phosphorus content, with the increases of 15.66%, 25.49%, 36.00%, and 18.42%, respectively. Among the nitrogen-reduction fertilization treatments, IT90 showed the most significant effect. Compared to IT, IT90 significantly increased R0.25, MWD, GMD, and available nitrogen content, with increases of 4.4%, 7.81%, 8.82%, and 28.89%, respectively. (2) Compared to RT, at the phylum level, the diversity of Chloroflexi was significantly increased under IT and IT50, and the diversity of Gemmatimonadota was significantly increased under IT90, IT70, and IT50. The diversity of Acidobacteriota was significantly higher in IT90 and IT70 compared to IT. It was shown that the rice–eel co-culture system and nitrogen fertilizer reduction could effectively improve the degradation capacity of organic matter and promote soil nitrogen cycling. In addition, redundancy analysis (RDA) identified total phosphorus, total nitrogen, and available nitrogen (p = 0.007) as the three most important environmental factors driving changes in the bacterial community. (3) The functional prediction analysis of soil microbiota showed that, compared to RT, the diversity of pathways related to biosynthesis (carbohydrate biosynthesis and cell structure biosynthesis) and metabolism (L-glutamate and L-glutamine biosynthesis) was significantly higher under IT70, IT90, IT, and IT50 (in descending order). However, the diversity of pathways associated with degradation/utilization/assimilation (secondary metabolite degradation and amine and polyamine degradation) was significantly lower under all the rice–eel co-culture treatments. In conclusion, the rice–eel co-culture system improved soil physicochemical properties and the soil microbial environment compared with conventional planting, and the best soil improvement was achieved with 10% less N fertilizer application. Full article
(This article belongs to the Special Issue Chemical Properties of Soils and its Impact on Plant Growth)
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18 pages, 7363 KiB  
Article
Agronomic Evaluation of Compost Formulations Based on Mining Tailings and Microbial Mats from Geothermal Sources
by María Jesús Puy-Alquiza, Miren Yosune Miranda Puy, Raúl Miranda-Avilés, Pooja Vinod Kshirsagar and Cristina Daniela Moncada Sanchez
Recycling 2025, 10(4), 156; https://doi.org/10.3390/recycling10040156 - 5 Aug 2025
Abstract
This study, conducted in Mexico, evaluates the agricultural potential of three compost formulations BFS1, BFS2, and BFS3 produced from mining tailings and thermophilic microbial mats and collected from geothermal environments. The physicochemical characterization included pH, electrical conductivity (EC), macronutrients (N, P, K, Ca, [...] Read more.
This study, conducted in Mexico, evaluates the agricultural potential of three compost formulations BFS1, BFS2, and BFS3 produced from mining tailings and thermophilic microbial mats and collected from geothermal environments. The physicochemical characterization included pH, electrical conductivity (EC), macronutrients (N, P, K, Ca, Mg, and S), micronutrients (Fe, Zn, B, Cu, Mn, Mo, and Ni), organic matter (OM), and the carbon-to-nitrogen (C/N) ratio. All composts exhibited neutral pH values (7.38–7.52), high OM content (38.5–48.4%), and optimal C/N ratios (10.5–13.9), indicating maturity and chemical stability. Nitrogen ranged from 19 to 21 kg·t−1, while potassium and calcium were present in concentrations beneficial for crop development. However, EC values (3.43–3.66 dS/m) and boron levels (>160 ppm) were moderately high, requiring caution in saline soils or with boron-sensitive crops. A semi-quantitative Compost Quality Index (CQI) ranked BFS3 highest due to elevated OM and potassium content, followed by BFS1. BFS2, while rich in nitrogen, scored lower due to excessive boron. One-way ANOVA revealed no significant difference in nitrogen (p > 0.05), but it did reveal significant differences in potassium (p < 0.01) and boron (p < 0.001) among formulations. These results confirm the potential of mining tailings—microbial mat composts are low-cost, nutrient-rich biofertilizers. They are suitable for field crops or as components in nursery substrates, particularly when EC and boron are managed through dilution. This study promotes the circular reuse of geothermal and industrial residues and contributes to sustainable soil restoration practices in mining-affected regions through innovative composting strategies. Full article
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14 pages, 764 KiB  
Article
Influence of Mineral Fertilizers and Application Methods on Raspberry Composition Cultivated in an Acid Soil
by Biljana Sikirić, Vesna Mrvić, Nikola Koković, Sonja Tošić Jojević, Mila Pešić, Nenad Prekop and Olivera Stajković-Srbinović
Horticulturae 2025, 11(8), 914; https://doi.org/10.3390/horticulturae11080914 (registering DOI) - 4 Aug 2025
Abstract
Acid soils are often a limiting factor in the production of most cultivated plants. In practice, the application of inadequate, physiologically acidic fertilizers, urea and NPK, is often encountered, which further worsens the already poor physicochemical properties of such soils. In this study, [...] Read more.
Acid soils are often a limiting factor in the production of most cultivated plants. In practice, the application of inadequate, physiologically acidic fertilizers, urea and NPK, is often encountered, which further worsens the already poor physicochemical properties of such soils. In this study, the influence of different amounts of NPK and urea fertilizers and methods of their application on the chemical properties of a very acidic soil and the accumulation of essential biogenic elements (N, P, K, Ca, Mg, and Al) in raspberry plants (leaves and fruits) was evaluated. The field trial with the raspberry plants was set up on a very acidic soil (pH in KCl 3.6), type Dystric Cambisol, and was monitored for 2 years. The application of NPK and urea mainly increased soil acidity in the second year in all treatments (for 0.10–0.18 pH unit) (except for urea applied in rows). The application of higher amounts of NPK increased the content of available forms of P (for 9.3–30.8 mg/kg) and K (for 57–95 mg/kg) in soil in both years, as well as exchangeable Ca (for 200–510 mg/kg) and Mg in the first year (15–165 mg/kg). The introduction of fertilizers in rows, compared to fertilization of the entire surface, influenced the reduction in mobile Al (especially when applying NPK, from 5.89 to 7.13 mg/100 g), the increase in mineral N and K content in the soil, and the increase in Ca and Mg only when applying urea, i.e., P when applying NPK in rows. In the leaves, the application of fertilizers in rows increased the content of Ca and Mg in the first year and P and K in the second year. In the fruits, the content of all estimated elements was not in correlation with their content in leaves and the fertilizer application, which indicates the influence of other ecological and biological factors on plant nutrition. Full article
(This article belongs to the Section Plant Nutrition)
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23 pages, 3221 KiB  
Article
Drought Modulates Root–Microbe Interactions and Functional Gene Expression in Plateau Wetland Herbaceous Plants
by Yuanyuan Chen, Shishi Feng, Qianmin Liu, Di Kang and Shuzhen Zou
Plants 2025, 14(15), 2413; https://doi.org/10.3390/plants14152413 - 4 Aug 2025
Abstract
In plateau wetlands, the interactions of herbaceous roots with ectorhizosphere soil microorganisms represent an important way to realize their ecological functions. Global change-induced aridification of plateau wetlands has altered long-established functional synergistic relationships between plant roots and ectorhizosphere soil microbes, but we still [...] Read more.
In plateau wetlands, the interactions of herbaceous roots with ectorhizosphere soil microorganisms represent an important way to realize their ecological functions. Global change-induced aridification of plateau wetlands has altered long-established functional synergistic relationships between plant roots and ectorhizosphere soil microbes, but we still know little about this phenomenon. In this context, nine typical wetlands with three different moisture statuses were selected from the eastern Tibetan Plateau in this study to analyze the relationships among herbaceous plant root traits and microbial communities and functions. The results revealed that drought significantly inhibited the accumulation of root biomass and surface area as well as the development of root volumes and diameters. Similarly, drought significantly reduced the diversity of ectorhizosphere soil microbial communities and the relative abundances of key phyla of archaea and bacteria. Redundancy analysis revealed that plant root traits and ectorhizosphere soil microbes were equally regulated by soil physicochemical properties. Functional genes related to carbohydrate metabolism were significantly associated with functional traits related to plant root elongation and nutrient uptake. Functional genes related to carbon and energy metabolism were significantly associated with traits related to plant root support and storage. Key genes such as CS,gltA, and G6PD,zwf help to improve the drought resistance and barrenness resistance of plant roots. This study helps to elucidate the synergistic mechanism of plant and soil microbial functions in plateau wetlands under drought stress, and provides a basis for evolutionary research and conservation of wetland ecosystems in the context of global change. Full article
(This article belongs to the Special Issue Soil-Beneficial Microorganisms and Plant Growth: 2nd Edition)
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21 pages, 3085 KiB  
Article
Poultry Manure-Derived Biochar Synthesis, Characterization, and Valorization in Agriculture: Effect of Pyrolysis Temperature and Metal-Salt Modification
by Samar Hadroug, Leila El-Bassi, Salah Jellali, Ahmed Amine Azzaz, Mejdi Jeguirim, Helmi Hamdi, James J. Leahy, Amine Aymen Assadi and Witold Kwapinski
Soil Syst. 2025, 9(3), 85; https://doi.org/10.3390/soilsystems9030085 (registering DOI) - 4 Aug 2025
Abstract
In the present work, six biochars were produced from the pyrolysis of poultry manure at 400 °C and 600 °C (PM-B-400 and PM-B-600), and their post-modification with, respectively, iron chloride (PM-B-400-Fe and PM-B-600-Fe) and potassium permanganate (PM-B-400-Mn and PM-B-600-Mn). First, these biochars were [...] Read more.
In the present work, six biochars were produced from the pyrolysis of poultry manure at 400 °C and 600 °C (PM-B-400 and PM-B-600), and their post-modification with, respectively, iron chloride (PM-B-400-Fe and PM-B-600-Fe) and potassium permanganate (PM-B-400-Mn and PM-B-600-Mn). First, these biochars were deeply characterized through the assessment of their particle size distribution, pH, electrical conductivity, pH at point-zero charge, mineral composition, morphological structure, and surface functionality and crystallinity, and then valorized as biofertilizer to grow spring barley at pot-scale for 40 days. Characterization results showed that Fe- and Mn-based nanoparticles were successfully loaded onto the surface of the post-modified biochars, which significantly enhanced their structural and surface chemical properties. Moreover, compared to the control treatment, both raw and post-modified biochars significantly improved the growth parameters of spring barley plants (shoot and root length, biomass weight, and nutrient content). The highest biomass production was obtained for the treatment with PM-B-400-Fe, owing to its enhanced physico-chemical properties and its higher ability in releasing nutrients and immobilizing heavy metals. These results highlight the potential use of Fe-modified poultry manure-derived biochar produced at low temperatures as a sustainable biofertilizer for soil enhancement and crop yield improvement, while addressing manure management issues. Full article
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19 pages, 6111 KiB  
Article
Impact of Water Conductivity on the Structure and Swelling Dynamics of E-Beam Cross-Linked Hydrogels
by Elena Mănăilă, Ion Călina, Anca Scărișoreanu, Maria Demeter, Gabriela Crăciun and Marius Dumitru
Gels 2025, 11(8), 611; https://doi.org/10.3390/gels11080611 - 4 Aug 2025
Abstract
Prolonged drought and soil degradation severely affect soil fertility and limit crop productivity. Superabsorbent hydrogels offer an effective solution for improving water retention in soil and supporting plant growth. In this work, we examined the performance of superabsorbent hydrogels based on sodium alginate, [...] Read more.
Prolonged drought and soil degradation severely affect soil fertility and limit crop productivity. Superabsorbent hydrogels offer an effective solution for improving water retention in soil and supporting plant growth. In this work, we examined the performance of superabsorbent hydrogels based on sodium alginate, acrylic acid (AA), and poly (ethylene oxide) (PEO) cross-linked with 12.5 kGy using e-beam irradiation. The hydrogels were assessed in various aqueous environments by examining network characteristics, swelling capacity, and swelling kinetics to evaluate the impact of water’s electrical conductivity (which ranges from 0.05 to 321 μS/cm). Morphological and chemical structure changes were evaluated using SEM and FTIR techniques. The results demonstrated that water conductivity significantly affected the physicochemical properties of the hydrogels. Swelling behavior showed notable sensitivity to electrical conductivity variations, with swelling degrees reaching 28,400% at 5 μS/cm and 14,000% at 321 μS/cm, following first-order and second-order kinetics. FTIR analysis confirmed that structural modifications correlated with water conductivity, particularly affecting the O–H, C–H, and COOH groups sensitive to the ionic environment. SEM characterization revealed a porous morphology with an interconnected microporous network that facilitates efficient water diffusion. These hydrogels show exceptional swelling capacity and are promising candidates for sustainable agriculture applications. Full article
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15 pages, 2885 KiB  
Article
Effects of Modified Senna obtusifolia Straw Biochar on Organic Matter Mineralization and Nutrient Transformation in Siraitia grosvenorii Farmland
by Lening Hu, Yinnan Bai, Shu Li, Gaoyan Liu, Jingxiao Liang, Hua Deng, Anyu Li, Linxuan Li, Limei Pan and Yuan Huang
Agronomy 2025, 15(8), 1877; https://doi.org/10.3390/agronomy15081877 - 3 Aug 2025
Viewed by 114
Abstract
Biochar has garnered considerable attention as a soil amendment due to its unique physicochemical properties. Its application not only enhances soil carbon sequestration but also improves nutrient availability. Incorporating biochar into soil is regarded as a promising strategy for mitigating global climate change [...] Read more.
Biochar has garnered considerable attention as a soil amendment due to its unique physicochemical properties. Its application not only enhances soil carbon sequestration but also improves nutrient availability. Incorporating biochar into soil is regarded as a promising strategy for mitigating global climate change while delivering substantial environmental and agricultural benefits. In this study, biochar was extracted from Siraitia grosvenorii and subsequently modified through alkali treatment. A laboratory incubation experiment was conducted to assess the effects of unmodified (JMC) and modified (GXC) biochar, applied at different rates (1%, 2%, and 4%), on organic carbon mineralization and soil nutrient dynamics. Results indicated that, at equivalent application rates, JMC-treated soils exhibited lower CO2 emissions than those treated with GXC, with emissions increasing alongside biochar dosage. After the incubation, the 1% JMC treatment exhibited a mineralization rate of 17.3 mg·kg−1·d−1, which was lower than that of the control (CK, 18.8 mg·kg−1·d−1), suggesting that JMC effectively inhibited organic carbon mineralization and reduced CO2 emissions, thereby contributing positively to carbon sequestration in Siraitia grosvenorii farmland. In contrast, GXC application significantly enhanced soil nutrient levels, particularly increasing available phosphorus (AP) by 14.33% to 157.99%. Furthermore, partial least squares structural equation modeling (PLS-SEM) identified application rate and pH as the key direct factors influencing soil nutrient availability. Full article
(This article belongs to the Section Soil and Plant Nutrition)
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26 pages, 3020 KiB  
Review
Fabrication of Cellulose-Based Hydrogels Through Ionizing Radiation for Environmental and Agricultural Applications
by Muhammad Asim Raza
Gels 2025, 11(8), 604; https://doi.org/10.3390/gels11080604 - 2 Aug 2025
Viewed by 146
Abstract
Hydrogels exhibit remarkable physicochemical properties, including high water absorption and retention capacities, as well as controlled release behavior. Their inherent biodegradability, biocompatibility, and non-toxicity make them suitable for a wide range of applications. Cellulose, a biodegradable, renewable, and abundantly available polysaccharide, is a [...] Read more.
Hydrogels exhibit remarkable physicochemical properties, including high water absorption and retention capacities, as well as controlled release behavior. Their inherent biodegradability, biocompatibility, and non-toxicity make them suitable for a wide range of applications. Cellulose, a biodegradable, renewable, and abundantly available polysaccharide, is a viable source for hydrogel preparation. Ionizing radiation, using electron-beam (EB) or gamma (γ) irradiation, provides a promising approach for synthesizing hydrogels. This study reviews recent advancements in cellulose-based hydrogels, focusing on cellulose and its derivatives, brief information regarding ionizing radiation, comparison between EB and γ-irradiation, synthesis and modification through ionizing radiation technology, and their environmental and agricultural applications. For environmental remediation, these hydrogels have demonstrated significant potential in water purification, particularly in the removal of heavy metals, dyes, and organic contaminants. In agricultural applications, cellulose-based hydrogels function as soil conditioners by enhancing water retention and serving as carriers for agrochemicals. Full article
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17 pages, 1792 KiB  
Review
The Response Mechanism of Soil Microbial Carbon Use Efficiency to Land-Use Change: A Review
by Zongkun Li and Dandan Qi
Sustainability 2025, 17(15), 7023; https://doi.org/10.3390/su17157023 - 2 Aug 2025
Viewed by 339
Abstract
Microbial carbon use efficiency (CUE) is an important indicator of soil organic carbon accumulation and loss and a key parameter in biogeochemical cycling models. Its regulatory mechanism is highly dependent on microbial communities and their dynamic mediation of abiotic factors. Land-use change (e.g., [...] Read more.
Microbial carbon use efficiency (CUE) is an important indicator of soil organic carbon accumulation and loss and a key parameter in biogeochemical cycling models. Its regulatory mechanism is highly dependent on microbial communities and their dynamic mediation of abiotic factors. Land-use change (e.g., agricultural expansion, deforestation, urbanization) profoundly alter carbon input patterns and soil physicochemical properties, further exacerbating the complexity and uncertainty of CUE. Existing carbon cycle models often neglect microbial ecological processes, resulting in an incomplete understanding of how microbial traits interact with environmental factors to regulate CUE. This paper provides a comprehensive review of the microbial regulation mechanisms of CUE under land-use change and systematically explores how microorganisms drive organic carbon allocation through community compositions, interspecies interactions, and environmental adaptability, with particular emphasis on the synergistic response between microbial communities and abiotic factors. We found that the buffering effect of microbial communities on abiotic factors during land-use change is a key factor determining CUE change patterns. This review not only provides a theoretical framework for clarifying the microbial-dominated carbon turnover mechanism but also lays a scientific foundation for the precise implementation of sustainable land management and carbon neutrality goals. Full article
(This article belongs to the Special Issue Soil Ecology and Carbon Cycle)
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16 pages, 3713 KiB  
Article
Synergistic Alleviation of Saline–Alkali Stress and Enhancement of Selenium Nutrition in Rice by ACC (1-Aminocyclopropane-1-Carboxylate) Deaminase-Producing Serratia liquefaciens and Biogenically Synthesized Nano-Selenium
by Nina Zhu, Xinpei Wei, Xingye Pan, Benkang Xie, Shuquan Xin and Kai Song
Plants 2025, 14(15), 2376; https://doi.org/10.3390/plants14152376 - 1 Aug 2025
Viewed by 144
Abstract
Soil salinization and selenium (Se) deficiency threaten global food security. This study developed a composite bioinoculant combining ACC deaminase-producing Serratia liquefaciens and biogenically synthesized nano-selenium (SeNPs) to alleviate saline–alkali stress and enhance Se nutrition in rice (Oryza sativa L.). A strain of [...] Read more.
Soil salinization and selenium (Se) deficiency threaten global food security. This study developed a composite bioinoculant combining ACC deaminase-producing Serratia liquefaciens and biogenically synthesized nano-selenium (SeNPs) to alleviate saline–alkali stress and enhance Se nutrition in rice (Oryza sativa L.). A strain of S. liquefaciens with high ACC deaminase activity was isolated and used to biosynthesize SeNPs with stable physicochemical properties. Pot experiments showed that application of the composite inoculant (S3: S. liquefaciens + 40 mmol/L SeNPs) significantly improved seedling biomass (fresh weight +53.8%, dry weight +60.6%), plant height (+31.6%), and root activity under saline–alkali conditions. S3 treatment also enhanced panicle weight, seed-setting rate, and grain Se content (234.13 μg/kg), meeting national Se-enriched rice standards. Moreover, it increased rhizosphere soil N, P, and K availability and improved microbial α-diversity. This is the first comprehensive demonstration that a synergistic bioformulation of ACC deaminase PGPR and biogenic SeNPs effectively mitigates saline–alkali stress, enhances soil fertility, and enables safe Se biofortification in rice. Full article
(This article belongs to the Special Issue Nanomaterials in Plant Growth and Stress Adaptation—2nd Edition)
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23 pages, 5040 KiB  
Article
Population Density and Diversity of Millipedes in Four Habitat Classes: Comparison Concerning Vegetation Type and Soil Characteristics
by Carlos Suriel, Julián Bueno-Villegas and Ulises J. Jauregui-Haza
Ecologies 2025, 6(3), 55; https://doi.org/10.3390/ecologies6030055 - 1 Aug 2025
Viewed by 170
Abstract
Our study was conducted in the Valle Nuevo National Park and included four habitat classes: tussock grass (Sabapa), pine forest (Pinoc), broadleaf forest (Boslat), and agricultural ecosystem (Ecoag). We had two main objectives: to comparatively describe millipede communities and to determine the relationships [...] Read more.
Our study was conducted in the Valle Nuevo National Park and included four habitat classes: tussock grass (Sabapa), pine forest (Pinoc), broadleaf forest (Boslat), and agricultural ecosystem (Ecoag). We had two main objectives: to comparatively describe millipede communities and to determine the relationships between population density/diversity and soil physicochemical variables. The research was cross-sectional and non-manipulative, with a descriptive and correlational scope; sampling followed a stratified systematic design, with eight transects and 32 quadrats of 1 m2, covering 21.7 km. We found a sandy loam soil with an extremely acidic pH. The highest population density of millipedes was recorded in Sabapa, and the lowest in Ecoag. The highest alpha diversity was shared between Boslat (Margalef = 1.72) and Pinoc (Shannon = 2.53); Sabapa and Boslat showed the highest Jaccard similarity (0.56). The null hypothesis test using the weighted Shannon index revealed a statistically significant difference in diversity between the Boslat–Sabapa and Pinoc–Sabapa pairs. Two of the species recorded highly significant indicator values (IndVal) for two habitat classes. We found significant correlations (p < 0.05) between various soil physicochemical variables and millipede density and diversity. Full article
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17 pages, 5265 KiB  
Article
Influence of Agricultural Practices on Soil Physicochemical Properties and Rhizosphere Microbial Communities in Apple Orchards in Xinjiang, China
by Guangxin Zhang, Zili Wang, Huanhuan Zhang, Xujiao Li, Kun Liu, Kun Yu, Zhong Zheng and Fengyun Zhao
Horticulturae 2025, 11(8), 891; https://doi.org/10.3390/horticulturae11080891 (registering DOI) - 1 Aug 2025
Viewed by 175
Abstract
In response to the challenges posed by soil degradation in the arid regions of Xinjiang, China, green and organic management practices have emerged as effective alternatives to conventional agricultural management methods, helping to mitigate soil degradation by promoting natural soil recovery and ecological [...] Read more.
In response to the challenges posed by soil degradation in the arid regions of Xinjiang, China, green and organic management practices have emerged as effective alternatives to conventional agricultural management methods, helping to mitigate soil degradation by promoting natural soil recovery and ecological balance. However, most of the existing studies focus on a single management practice or indicator and lack a systematic assessment of the effects of integrated orchard management in arid zones. This study aims to investigate how different agricultural management practices influence soil physicochemical properties and inter-root microbial communities in apple orchards in Xinjiang and to identify the main physicochemical factors affecting the composition of inter-root microbial communities. Inter-root soil samples were collected from apple orchards under green management (GM), organic management (OM), and conventional management (CM) in major apple-producing regions of Xinjiang. Microbial diversity and community composition of the samples were analyzed using high-throughput amplicon sequencing. The results revealed significant differences (p < 0.05) in soil physicochemical properties across different management practices. Specifically, GM significantly reduced soil pH and C:N compared with OM. Both OM and GM significantly decreased soil available nutrient content compared with CM. Moreover, GM and OM significantly increased bacterial diversity and changed the community composition of bacteria and fungi. Proteobacteria and Ascomycota were identified as the dominant bacteria and fungi, respectively, in all management practices. Linear discriminant analysis (LEfSe) showed that biomarkers were more abundant under OM, suggesting that OM may contribute to ecological functions through specific microbial taxa. Co-occurrence network analysis (building a network of microbial interactions) demonstrated that the topologies of bacteria and fungi varied across different management practices and that OM increased the complexity of microbial co-occurrence networks. Mantel test analysis (analyzing soil factors and microbial community correlations) showed that C:N and available potassium (AK) were significantly and positively correlated with the community composition of bacteria and fungi, and that C:N, soil organic carbon (SOC), and alkaline hydrolyzable nitrogen (AN) were significantly and positively correlated with the diversity of fungi. Redundancy analysis (RDA) further indicated that SOC, C:N, and AK were the primary soil physicochemical factors influencing the composition of microbial communities. This study provides theoretical guidance for the sustainable management of orchards in arid zones. Full article
(This article belongs to the Section Fruit Production Systems)
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20 pages, 2782 KiB  
Article
Urban Forest Fragmentation Reshapes Soil Microbiome–Carbon Dynamics
by Melinda Haydee Kovacs, Nguyen Khoi Nghia and Emoke Dalma Kovacs
Diversity 2025, 17(8), 545; https://doi.org/10.3390/d17080545 - 1 Aug 2025
Viewed by 144
Abstract
Urban expansion fragments once-contiguous forest patches, generating pronounced edge gradients that modulate soil physicochemical properties and biodiversity. We quantified how fragmentation reshaped the soil microbiome continuum and its implications for soil carbon storage in a temperate urban mixed deciduous forest. A total of [...] Read more.
Urban expansion fragments once-contiguous forest patches, generating pronounced edge gradients that modulate soil physicochemical properties and biodiversity. We quantified how fragmentation reshaped the soil microbiome continuum and its implications for soil carbon storage in a temperate urban mixed deciduous forest. A total of 18 plots were considered in this study, with six plots for each fragment type. Intact interior forest (F), internal forest path fragment (IF), and external forest path fragment (EF) soils were sampled at 0–15, 15–30, and 30–45 cm depths and profiled through phospholipid-derived fatty acid (PLFA) chemotyping and amino sugar proxies for living microbiome and microbial-derived necromass assessment, respectively. Carbon fractionation was performed through the chemical oxidation method. Diversity indices (Shannon–Wiener, Pielou evenness, Margalef richness, and Simpson dominance) were calculated based on the determined fatty acids derived from the phospholipid fraction. The microbial biomass ranged from 85.1 to 214.6 nmol g−1 dry soil, with the surface layers of F exhibiting the highest values (p < 0.01). Shannon diversity declined systematically from F > IF > EF. The microbial necromass varied from 11.3 to 23.2 g⋅kg−1. Fragmentation intensified the stratification of carbon pools, with organic carbon decreasing by approximately 14% from F to EF. Our results show that EFs possess a declining microbiome continuum that weakens their carbon sequestration capacity in urban forests. Full article
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22 pages, 7580 KiB  
Article
Bacterial and Physicochemical Dynamics During the Vermicomposting of Bovine Manure: A Comparative Analysis of the Eisenia fetida Gut and Compost Matrix
by Tania Elizabeth Velásquez-Chávez, Jorge Sáenz-Mata, Jesús Josafath Quezada-Rivera, Rubén Palacio-Rodríguez, Gisela Muro-Pérez, Alan Joel Servín-Prieto, Mónica Hernández-López, Pablo Preciado-Rangel, María Teresa Salazar-Ramírez, Juan Carlos Ontiveros-Chacón and Cristina García-De la Peña
Microbiol. Res. 2025, 16(8), 177; https://doi.org/10.3390/microbiolres16080177 - 1 Aug 2025
Viewed by 92
Abstract
Vermicomposting is a sustainable biotechnological process that transforms organic waste through the synergistic activity of earthworms, such as Eisenia fetida, and their associated microbiota. This study evaluated bacterial and physicochemical dynamics during the vermicomposting of bovine manure by analyzing the microbial composition [...] Read more.
Vermicomposting is a sustainable biotechnological process that transforms organic waste through the synergistic activity of earthworms, such as Eisenia fetida, and their associated microbiota. This study evaluated bacterial and physicochemical dynamics during the vermicomposting of bovine manure by analyzing the microbial composition of the substrate and the gut of E. fetida at three time points (weeks 0, 6, and 12). The V3–V4 region of the 16S rRNA gene was sequenced, and microbial diversity was characterized using QIIME2. Significant differences in alpha diversity (observed features, Shannon index, and phylogenetic diversity) and beta diversity indicated active microbial succession. Proteobacteria, Bacteroidota, and Actinobacteriota were the dominant phyla, with abundances varying across habitats and over time. A significant enrichment of Proteobacteria, Bacteroidota, and the genera Chryseolinea, Flavobacterium, and Sphingomonas was observed in the manure treatments. In contrast, Actinobacteriota, Firmicutes, and the genera Methylobacter, Brevibacillus, Enhygromyxa, and Bacillus, among others, were distinctive of the gut samples and contributed to their dissimilarity from the manure treatments. Simultaneously, the physicochemical parameters indicated progressive substrate stabilization and nutrient enrichment. Notably, the organic matter and total organic carbon contents decreased (from 79.47% to 47.80% and from 46.10% to 27.73%, respectively), whereas the total nitrogen content increased (from 1.70% to 2.23%); these effects reduced the C/N ratio, which is a recognized indicator of maturity, from 27.13 to 12.40. The macronutrient contents also increased, with final values of 1.41% for phosphorus, 1.50% for potassium, 0.89% for magnesium, and 2.81% for calcium. These results demonstrate that vermicomposting modifies microbial communities and enhances substrate quality, supporting its use as a biofertilizer for sustainable agriculture, soil restoration, and agrochemical reduction. Full article
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21 pages, 1538 KiB  
Article
Soil Fungal Activity and Microbial Response to Wildfire in a Dry Tropical Forest of Northern Colombia
by Eliana Martínez Mera, Ana Carolina Torregroza-Espinosa, Ana Cristina De la Parra-Guerra, Marielena Durán-Castiblanco, William Zapata-Herazo, Juan Sebastián Rodríguez-Rebolledo, Fernán Zabala-Sierra and David Alejandro Blanco Alvarez
Diversity 2025, 17(8), 546; https://doi.org/10.3390/d17080546 - 1 Aug 2025
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Abstract
Wildfires can significantly alter soil physicochemical conditions and microbial communities in forest ecosystems. This study aimed to characterize the culturable soil fungal community and evaluate biological activity in Banco Totumo Bijibana, a protected dry tropical forest in Atlántico, Colombia, affected by a wildfire [...] Read more.
Wildfires can significantly alter soil physicochemical conditions and microbial communities in forest ecosystems. This study aimed to characterize the culturable soil fungal community and evaluate biological activity in Banco Totumo Bijibana, a protected dry tropical forest in Atlántico, Colombia, affected by a wildfire in 2014. Twenty soil samples were collected for microbiological (10 cm depth) and physicochemical (30 cm) analysis. Basal respiration was measured using Stotzky’s method, nitrogen mineralization via Rawls’ method, and fungal diversity through culture-based identification and colony-forming unit (CFU) counts. Diversity was assessed using Simpson, Shannon–Weaver, and ACE indices. The soils presented low organic matter (0.70%) and nitrogen content (0.035%), with reduced biological activity as indicated by basal respiration (0.12 kg C ha−1 d−1) and mineralized nitrogen (5.61 kg ha−1). Four fungal morphotypes, likely from the genus Aspergillus, were identified. Simpson index indicated moderate dominance, while Shannon–Weaver values reflected low diversity. Correlation analysis showed Aspergillus-3 was positively associated with moisture, whereas Aspergillus-4 correlated negatively with pH and sand content. The species accumulation curve reached an asymptote, suggesting an adequate sampling effort. Although no control site was included, the findings provide a baseline characterization of post-fire soil microbial structure and function in a dry tropical ecosystem. Full article
(This article belongs to the Section Microbial Diversity and Culture Collections)
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