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Keywords = Chloroflexi

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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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13 pages, 1075 KiB  
Article
Response of Typical Artificial Forest Soil Microbial Community to Revegetation in the Loess Plateau, China
by Xiaohua Liu, Tianxing Wei, Dehui Fan, Huaxing Bi and Qingke Zhu
Agronomy 2025, 15(8), 1821; https://doi.org/10.3390/agronomy15081821 - 28 Jul 2025
Viewed by 212
Abstract
This study aims to analyze the differences in soil bacterial community structure under different vegetation restoration types, and to explore the role of microorganisms in the process of vegetation restoration on the soil ecosystem of the Grain for Green area in the Loess [...] Read more.
This study aims to analyze the differences in soil bacterial community structure under different vegetation restoration types, and to explore the role of microorganisms in the process of vegetation restoration on the soil ecosystem of the Grain for Green area in the Loess Plateau. High-throughput sequencing technology was used to analyze the alpha diversity of soil bacteria, community structure characteristics, and the correlation between soil environmental factors and bacterial communities in different artificial Hippophae rhamnoides forests. Soil microbial C and N show a decreasing trend with an increase in the 0–100 cm soil layers. The results indicated that the bacterial communities comprised 24 phyla, 55 classes, 110 orders, 206 families, 348 genera, 680 species, and 1989 OTUs. Additionally, the richness indices and diversity indices of the bacterial community in arbor shrub mixed forest are higher than those in shrub pure forest, and the indices of shrub forest on sunny slope are higher than those on shady slope. Across all samples, the dominant groups were Actinobacteria (37.27% on average), followed by Proteobacteria (23.91%), Acidobacteria (12.75%), and Chloroflexi (12.27%). Soil nutrient supply, such as TOC, TN, AN, AP, and AK, had crucial roles in shaping the composition and diversity of the bacterial communities. The findings reveal that vegetation restoration significantly affected soil bacterial community richness and diversity. Furthermore, based on the results, our data provide a starting point for establishing soil bacterial databases in the Loess Plateau, as well as for the plants associated with the vegetation restoration. Full article
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18 pages, 4241 KiB  
Article
Distribution Patterns and Assembly Mechanisms of Rhizosphere Soil Microbial Communities in Schisandra sphenanthera Across Altitudinal Gradients
by Weimin Li, Luyao Yang, Xiaofeng Cong, Zhuxin Mao and Yafu Zhou
Biology 2025, 14(8), 944; https://doi.org/10.3390/biology14080944 - 27 Jul 2025
Viewed by 246
Abstract
To investigate the characteristics of rhizosphere soil microbial communities associated with Schisandra sphenanthera across different altitudinal gradients and to reveal the driving factors of microbial community dynamics, this study collected rhizosphere soil samples at four elevations: 900 m (HB1), 1100 m (HB2), 1300 [...] Read more.
To investigate the characteristics of rhizosphere soil microbial communities associated with Schisandra sphenanthera across different altitudinal gradients and to reveal the driving factors of microbial community dynamics, this study collected rhizosphere soil samples at four elevations: 900 m (HB1), 1100 m (HB2), 1300 m (HB3), and 1500 m (HB4). High-throughput sequencing and molecular ecological network analysis were employed to analyze the microbial community composition and species interactions. A null model was applied to elucidate community assembly mechanisms. The results demonstrated that bacterial communities were dominated by Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi. The relative abundance of Proteobacteria increased with elevation, while that of Acidobacteriota and Actinobacteriota declined. Fungal communities were primarily composed of Ascomycota and Basidiomycota, with both showing elevated relative abundances at higher altitudes. Diversity indices revealed that HB2 exhibited the highest bacterial Chao, Ace, and Shannon indices but the lowest Simpson index. For fungi, HB3 displayed the highest Chao and Ace indices, whereas HB4 showed the highest Shannon index and the lowest Simpson index. Ecological network analysis indicated stronger bacterial competition at lower elevations and enhanced cooperation at higher elevations, contrasting with fungal communities that exhibited increased competition at higher altitudes. Altitude and soil nutrients were negatively correlated with soil carbon content, while plant nutrients and fungal diversity positively correlated with soil carbon. Null model analysis suggested that deterministic processes dominated bacterial community assembly, whereas stochastic processes governed fungal assembly. These findings highlight significant altitudinal shifts in the microbial community structure and assembly mechanisms in S. sphenanthera rhizosphere soils, driven by the synergistic effects of soil nutrients, plant growth, and fungal diversity. This study provides critical insights into microbial ecology and carbon cycling in alpine ecosystems, offering a scientific basis for ecosystem management and conservation. Full article
(This article belongs to the Section Ecology)
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12 pages, 1633 KiB  
Article
Responses of Rhizospheric Microbial Communities to Brevibacillus laterosporus-Enhanced Reductive Soil Disinfestation in Continuous Cropping Systems
by Risheng Xu, Haijiao Liu, Yafei Chen, Zhen Guo, Juan Liu, Yue Li, Jingyi Mei, Tengfei Ma and Yanlong Chen
Agronomy 2025, 15(8), 1775; https://doi.org/10.3390/agronomy15081775 - 24 Jul 2025
Viewed by 232
Abstract
Reductive soil disinfestation (RSD) significantly alters soil characteristics, yet its combined effects with bacterial inoculation on subsequent rhizospheric microbial community composition remains poorly understood. To address this knowledge gap, we investigated the effects of RSD and endophytic Brevibacillus laterosporus inoculation on the composition, [...] Read more.
Reductive soil disinfestation (RSD) significantly alters soil characteristics, yet its combined effects with bacterial inoculation on subsequent rhizospheric microbial community composition remains poorly understood. To address this knowledge gap, we investigated the effects of RSD and endophytic Brevibacillus laterosporus inoculation on the composition, network, and predicted function of peanut rhizospheric bacteria and fungi. Our results demonstrated that RSD and B. laterosporus inoculation substantially increased rhizospheric bacterial diversity while reducing fungal diversity. Specifically, B. laterosporus-enhanced RSD significantly reshaped the bacterial community, resulting in increased relative abundances of Chloroflexi, Desulfobacterota, and Myxococcota while decreasing those of Firmicutes, Gemmatimonadota, and Acidobacteriota. The fungal community exhibited a more consistent response to RSD and B. laterosporus amendment, with reduced proportions of Ascomycota and Gemmatimonadota but an increase in Chytridiomycota. Network analysis revealed that B. laterosporus inoculation and RSD enhanced the bacterial species complexity and keystone taxa. Furthermore, canonical correspondence analysis indicated strong associations between the soil bacterial community and soil properties, including Eh, EC, NO3-N, and SOC. Our findings highlight that the shifts in bacterial taxa induced by B. laterosporus inoculation and RSD, particularly the keystone taxa identified in the network, may contribute to the suppression of soil-borne pathogens. Overall, this study provides a novel insight into the shifts in rhizospheric bacterial and fungal communities and their ecological functions after bacteria inoculation and RSD treatment. Full article
(This article belongs to the Section Agricultural Biosystem and Biological Engineering)
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20 pages, 2995 KiB  
Article
Analysis of Bacterial Community During Cow Manure and Wheat Straw Composting and the Isolation of Lignin-Degrading Bacteria from the Compost
by Hanxiang Yang, Jianguo Hu, Bingxin Zhang, Yan Li, Chenxian Yang, Fusheng Chen, Tingwei Zhu and Ying Xin
Microorganisms 2025, 13(8), 1716; https://doi.org/10.3390/microorganisms13081716 - 22 Jul 2025
Viewed by 371
Abstract
Biodegradation is a green and efficient method for lignin depolymerization and conversion. In order to screen potential bacterial strains for efficient lignin degradation, composts of cow dung and wheat straw were prepared, and the dynamic changes in the predicted bacterial community structure and [...] Read more.
Biodegradation is a green and efficient method for lignin depolymerization and conversion. In order to screen potential bacterial strains for efficient lignin degradation, composts of cow dung and wheat straw were prepared, and the dynamic changes in the predicted bacterial community structure and function in different periods of the composts were investigated. Then, bacteria with an efficient lignin degradation ability were finally screened out from the compost samples. Based on the monitoring results of the physicochemical indexes of the composting process, it was found that the temperature and pH of the compost firstly increased and then decreased with the extension of time, and the water content and C/N gradually decreased. High-throughput sequencing of compost samples from the initial (DA), high-temperature (DB), and cooling (DC) periods revealed that the number of OTUs increased sharply then stabilized around 2000, and the alpha diversity of the bacterial community decreased firstly and then increased. The predominant phyla identified included Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes, determined by the relative abundance of beta-diversity-associated species. Functional gene analysis conducted using Tax4Fun revealed that the genes were primarily categorized into Metabolism, Genetic Information Processing, Environmental Information Processing, and Cellular Processes. Based on the decolorization of aniline blue and the degradation efficiency of alkali lignin, eight bacterial strains were isolated from compost samples at the three stages. Cupriavidus sp. F1 showed the highest degradation of alkali lignin with 66.01%. Cupriavidus sp. D8 showed the highest lignin degradation potential with all three enzyme activities significantly higher than the other strains. The results provide a strategy for the lignin degradation and utilization of biomass resources. Full article
(This article belongs to the Section Microbial Biotechnology)
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29 pages, 4742 KiB  
Article
Sustainable Tea Cultivation with a Rhizobacterial Consortium: A Microbiome-Driven Alternative to Chemical Fertilizers
by Silpi Sorongpong, Sourav Debnath, Praveen Rahi, Biswajit Bera and Piyush Pandey
Microorganisms 2025, 13(8), 1715; https://doi.org/10.3390/microorganisms13081715 - 22 Jul 2025
Viewed by 967
Abstract
The excessive use of chemical fertilizers in tea cultivation threatens soil health, environmental sustainability, and long-term crop productivity. This study explores the application of plant growth-promoting bacteria (PGPB) as an eco-friendly alternative to conventional fertilizers. A bacterial consortium was developed using selected rhizobacterial [...] Read more.
The excessive use of chemical fertilizers in tea cultivation threatens soil health, environmental sustainability, and long-term crop productivity. This study explores the application of plant growth-promoting bacteria (PGPB) as an eco-friendly alternative to conventional fertilizers. A bacterial consortium was developed using selected rhizobacterial isolates—Lysinibacillus fusiformis, five strains of Serratia marcescens, and two Bacillus spp.—based on their phosphate and zinc solubilization abilities and production of ACC deaminase, indole-3-acetic acid, and siderophores. The consortium was tested in both pot and field conditions using two tea clones, S3A3 and TS491, and compared with a chemical fertilizer treatment. Plants treated with the consortium showed enhanced growth, biomass, and antioxidant activity. The total phenolic contents increased to 1643.6 mg GAE/mL (S3A3) and 1646.93 mg GAE/mL (TS491), with higher catalase (458.17–458.74 U/g/min), glutathione (34.67–42.67 µmol/gfw), and superoxide dismutase (679.85–552.28 units/gfw/s) activities. A soil metagenomic analysis revealed increased microbial diversity and the enrichment of phyla, including Acidobacteria, Proteobacteria, Actinobacteria, Chloroflexi, and Firmicutes. Functional gene analysis showed the increased abundance of genes for siderophore biosynthesis, glutathione and nitrogen metabolism, and indole alkaloid biosynthesis. This study recommends the potential of a PGPB consortium as a sustainable alternative to chemical fertilizers, enhancing both the tea plant performance and soil microbial health. Full article
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21 pages, 5490 KiB  
Article
Impact of Reduced Chemical Fertilizer and Organic Amendments on Yield, Nitrogen Use Efficiency, and Soil Microbial Dynamics in Chinese Flowering Cabbage
by Jiaxin Xu, Jianshe Li, Xia Zhao, Zhen Liu, Hao Xu, Kai Cao and Lin Ye
Horticulturae 2025, 11(7), 859; https://doi.org/10.3390/horticulturae11070859 - 21 Jul 2025
Viewed by 306
Abstract
(1) Background: The escalating issue of soil degradation caused by excessive chemical fertilizer application poses significant threats to the sustainable development of Chinese flowering cabbage (Brassica campestris L. ssp. chinensis (L.) var. utilis Tsen et Lee) production. This research aimed to identify [...] Read more.
(1) Background: The escalating issue of soil degradation caused by excessive chemical fertilizer application poses significant threats to the sustainable development of Chinese flowering cabbage (Brassica campestris L. ssp. chinensis (L.) var. utilis Tsen et Lee) production. This research aimed to identify the impacts of reduced chemical fertilizer application integrated with organic amendments on cabbage yield and rhizosphere soil microenvironment characteristics. (2) Methods: A biennial field experiment was conducted during the 2022–2023 growing seasons at Lijun Town, Yinchuan City, Ningxia Hui Autonomous Region. Five treatments were tested: (i) Control (CK, no fertilizer); (ii) Conventional chemical fertilization (CF1, chemical fertilizer only); (iii) Reduced chemical fertilization (CF2, 30% less chemical fertilizer); (iv) CF2 + Well-decomposed chicken manure (FCM, 30% less chemical fertilizer + rotted chicken manure); and (v) CF2 + Vermicompost (FEM, 30% less chemical fertilizer + vermicompost). (3) Results: In 2023, the FCM treatment reduced electrical conductivity (EC) by 24.80% and pH by 2.16%, while the FEM treatment decreased EC by 31.13% and pH by 3.84% compared to controls. The FEM treatment significantly enhanced total nitrogen content by 12.71% and 8.85% relative to CF1 and FCM treatments, respectively. Compared to CF1, FEM increased soil organic matter content by 10.49% in 2022 and 11.24% in 2023. Organic fertilizer amendments elevated available nitrogen, phosphorus, and potassium levels while enhancing sucrase activity: FCM and FEM treatments increased sucrase activity by 23.62% and 32.00%, respectively, in 2022. Organic fertilization improved bacterial diversity and richness, optimized microbial community structure, and increased the relative abundance of Bacillus. It also upregulated microbial metabolic pathways related to carbohydrate and amino acid metabolism. Soil nutrients and bacterial community structure showed positive correlations with yield, whereas soil enzyme activities exhibited negative correlations. Key factors influencing yield were identified as Proteobacteria, Chloroflexi, available potassium, organic matter, available nitrogen, Actinobacteria, Firmicutes, total nitrogen, pH, and sucrase activity. (4) Conclusions: Integrated analysis of yield and soil microenvironmental parameters demonstrates that the fertilization regimen combining 30% chemical fertilizer reduction with vermicompost amendment (FEM) constitutes a more efficient fertilization strategy for Chinese flowering cabbage, making it suitable for regional promotion in the Ningxia area. Full article
(This article belongs to the Section Plant Nutrition)
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23 pages, 7168 KiB  
Article
Enhancing Soil Phosphorus Availability in Intercropping Systems: Roles of Plant Growth Regulators
by Chunhua Gao, Weilin Kong, Fengtao Zhao, Feiyan Ju, Ping Liu, Zongxin Li, Kaichang Liu and Haijun Zhao
Agronomy 2025, 15(7), 1748; https://doi.org/10.3390/agronomy15071748 - 20 Jul 2025
Viewed by 322
Abstract
Plant growth regulators (PGRs) enhance crop stress resistance but their roles in microbial-mediated phosphorus cycling within intercropping systems are unclear. Thus, We conducted a two-year field study using corn (Zea mays L. cv. Denghai 605) and soybean (Glycine max L. cv. [...] Read more.
Plant growth regulators (PGRs) enhance crop stress resistance but their roles in microbial-mediated phosphorus cycling within intercropping systems are unclear. Thus, We conducted a two-year field study using corn (Zea mays L. cv. Denghai 605) and soybean (Glycine max L. cv. Hedou 22) in fluvisols and luvisols soil according to World Reference Base for Soil Resources (WRB) standard. Under a 4-row corn and 6-row soybean strip intercropping system, three treatments were applied: a water control (CK), and two plant growth regulators—T1 (EC: ethephon [300 mg/L] + cycocel [2 g/L]) and T2 (ED: ethephon [300 mg/L] + 2-Diethyl aminoethyl hexanoate [10 mg/L]). Foliar applications were administered at the V7 stage (seventh leaf) of intercropped corn plants to assess how foliar-applied PGRs (T1/T2) modulated the soil phosphorus availability, microbial communities, and functional genes in maize intercropping systems. PGRs increased the soil organic phosphorus and available phosphorus contents, and alkaline phosphatase activity, but not total phosphorus. PGRs declined the α-diversity in fluvisols soil but increased the α-diversity in luvisols soil. The major taxa changed from Actinobacteria (CK) to Proteobacteria (T1) and Saccharibacteria (T2) in fluvisols soil, and from Actinobacteria/Gemmatimonadetes (CK) to Saccharibacteria (T1) and Acidobacteria (T2) in luvisols soil. Functional gene dynamics indicated soil-specific regulation, where fluvisols soil harbored more phoD (organic phosphorus mineralization) and relA (polyphosphate degradation) genes, whereas phnP gene dominated in luvisols soil. T1 stimulated organic phosphorus mineralization and inorganic phosphorus solubilization in fluvisols soil, upregulating regulation genes, and T2 enhanced polyphosphate synthesis and transport gene expression in luvisols soil. Proteobacteria, Nitrospirae, and Chloroflexi were positively correlated with organic phosphorus mineralization and polyphosphate cycling genes, whereas Bacteroidetes and Verrucomicrobia correlated with available potassium (AP), total phosphorus (TP), and alkaline phosphatase (ALP) activity. Thus, PGRs activated soil phosphorus by restructuring soil type-dependent microbial functional networks, connecting PGRs-induced shifts with microbial phosphorus cycling mechanisms. These findings facilitate the targeted use of PGRs to optimize microbial-driven phosphorus efficiency in strategies for sustainable phosphorus management in diverse agricultural soils. Full article
(This article belongs to the Section Innovative Cropping Systems)
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27 pages, 3832 KiB  
Article
Regulation of the Microbiome in Soil Contaminated with Diesel Oil and Gasoline
by Agata Borowik, Jadwiga Wyszkowska, Magdalena Zaborowska and Jan Kucharski
Int. J. Mol. Sci. 2025, 26(13), 6491; https://doi.org/10.3390/ijms26136491 - 5 Jul 2025
Viewed by 303
Abstract
Petroleum-derived contaminants pose a significant threat to the soil microbiome. Therefore, it is essential to explore materials and techniques that can restore homeostasis in disturbed environments. The aim of the study was to assess the response of the soil microbiome to contamination with [...] Read more.
Petroleum-derived contaminants pose a significant threat to the soil microbiome. Therefore, it is essential to explore materials and techniques that can restore homeostasis in disturbed environments. The aim of the study was to assess the response of the soil microbiome to contamination with diesel oil (DO) and gasoline (G) and to determine the capacity of sorbents, vermiculite (V), dolomite (D), perlite (P) and agrobasalt (A), to enhance the activity of microorganisms under Zea mays cultivation conditions in pot experiments. The restoration and activity of the soil microbiome were evaluated based on the abundance and diversity of bacteria and fungi, using both classical microbiological methods and Next Generation Sequencing (NGS). Bioinformatic tools were employed to calculate the physicochemical properties of proteins. DO increased the abundance of cultured microorganisms, whereas G significantly reduced it. Both DO and G increased the number of ASVs of Proteobacteria and decreased the relative abundance of Gemmatimonadetes, Chloroflexi, Acidobacteria, Verrucomicrobia, Planctomycetes, and fungal OTUs. These contaminants stimulated the growth of bacteria from the genera Rhodanobacter, Sphingomonas, Burkholderia, Sphingobium, and Mycobacterium, as well as fungi belonging to the Penicillium genus. Conversely, they had a negative effect on Kaistobacter, Rhodoplanes, and Ralstonia, as well as the fungi Chaetomium, Pseudaleuria, and Mortierella. DO caused greater changes in microbial alpha diversity than G. The stability of microbial proteins was higher at 17 °C than at −1 °C. The most stable proteins were found in bacteria and fungi identified within the core soil microbiome. These organisms exhibited greater diversity and more compact RNA secondary structures. The application of sorbents to contaminated soil altered the composition of bacterial and fungal communities. All sorbents enhanced the growth of organotrophic bacteria (Org) and fungi (Fun) in DO-contaminated soils, and actinobacteria (Act) and fungi in G-contaminated soils. V and A had the most beneficial effects on cultured microorganisms. In DO-contaminated soils, all sorbents inhibited the growth of Rhodanobacter, Parvibaculum, Sphingomonas, and Burkholderia, while stimulating Salinibacterium and Penicillium. In G-contaminated but otherwise unamended soils, all sorbents negatively affected the growth of Burkholderia, Sphingomonas, Kaistobacter, Rhodoplanes, Pseudonocardia, and Ralstonia and increased the abundance of Gymnostellatospora. The results of this study provide a valuable foundation for developing effective strategies to remediate soils contaminated with petroleum-derived compounds. Full article
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22 pages, 4025 KiB  
Article
Effects of Different Land Use Types on Soil Quality and Microbial Diversity in Paddy Soil
by Ximei Zhao, Fengyun Xiang, Xicheng Wang, Mengchen Yang and Jifu Li
Agronomy 2025, 15(7), 1628; https://doi.org/10.3390/agronomy15071628 - 3 Jul 2025
Viewed by 365
Abstract
This study investigated the effects of three land use patterns—rice (Oryza sativa L.)–rapeseed (Brassica napus L.) rotation (Rapeseed), rice–shrimp (Procambarus clarkii G.) rotation (Shrimp), and the conversion of paddy fields to forestland (Forestland)—on aggregate structure, nutrient content, and microbial diversity in [...] Read more.
This study investigated the effects of three land use patterns—rice (Oryza sativa L.)–rapeseed (Brassica napus L.) rotation (Rapeseed), rice–shrimp (Procambarus clarkii G.) rotation (Shrimp), and the conversion of paddy fields to forestland (Forestland)—on aggregate structure, nutrient content, and microbial diversity in rice soils in Chuandian Town, Jingzhou District, Jianghan Plain, central China. The results revealed that the Shrimp treatment significantly increased soil organic matter (SOM), available nitrogen (AN), and available phosphorus (AP) content in the surface soil (0–10 cm) while reducing soil bulk density and improving pore structure. Forestland exhibited higher aggregate stability in deeper soil layers (20–40 cm), particularly in the 0.053–0.25 mm size fraction. Microbial diversity analysis showed that bacterial richness (Chao1 index) and diversity (Shannon index) were significantly higher in the Shrimp and Rapeseed treatments compared to those in the Forestland treatment, with Proteobacteria and Chloroflexi being the dominant bacterial phyla. Fungal communities were dominated by Ascomycota, withfForestland showing greater fungal richness in deeper soil. Soil depth significantly influenced aggregates, nutrients, and microbial diversity, with surface soil exhibiting higher values for these parameters than deeper layers. Redundancy analysis indicated that SOM, AP, and pH were the key drivers of bacterial community variation, while fungal communities were more influenced by nitrogen and porosity. Path analysis further demonstrated that land use patterns indirectly affected microbial diversity via altering aggregate structure and nutrient availability. Overall, the Shrimp treatment outperformed others in improving soil structure and nutrient supply, whereas the Forestland treatment was more conducive to promoting aggregate stability in deeper soil. Land use patterns indirectly regulated microbial communities through modifying soil aggregate structure and nutrient status, thereby influencing soil ecosystem health and stability. This study provides a theoretical basis for the sustainable management of rice soils, suggesting the optimization of rotation patterns in agricultural production to synergistically enhance soil physical, chemical, and biological properties. Full article
(This article belongs to the Section Agroecology Innovation: Achieving System Resilience)
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21 pages, 2738 KiB  
Article
Effects of Fire on Soil Bacterial Communities and Nitrogen Cycling Functions in Greater Khingan Mountains Larch Forests
by Yang Shu, Wenjie Jia, Pengwu Zhao, Mei Zhou and Heng Zhang
Forests 2025, 16(7), 1094; https://doi.org/10.3390/f16071094 - 2 Jul 2025
Viewed by 350
Abstract
Investigating the effects of fire disturbance on soil microbial diversity and nitrogen cycling is crucial for understanding the mechanisms underlying soil nitrogen cycling. This study examined the fire burn site of the Larix gmelinii forest in the Greater Khingan Mountains, Inner Mongolia, to [...] Read more.
Investigating the effects of fire disturbance on soil microbial diversity and nitrogen cycling is crucial for understanding the mechanisms underlying soil nitrogen cycling. This study examined the fire burn site of the Larix gmelinii forest in the Greater Khingan Mountains, Inner Mongolia, to analyze the impact of varying fire intensities on soil nitrogen, microbial communities, and the abundance of nitrogen cycle-related functional genes after three years. The results indicated the following findings: (1) Soil bulk density increased significantly following severe fires (7.06%~10.84%, p < 0.05), whereas soil water content decreased with increasing fire intensity (6.62%~19.42%, p < 0.05). The soil total nitrogen and ammonium nitrogen levels declined after heavy fires but increased after mild fires; (2) Mild fire burning significantly increased soil bacterial diversity, while heavy fire had a lesser effect. Dominant bacterial groups included Xanthobacteraceae, norank_o_norank_c_AD3, and norank_o_Elsterales. Norank_o_norank_c_AD3 abundance decreased with burn intensity (7.90% unburned, 3.02% mild fire, 2.70% heavy fire). Conversely, norank_o_Elsterales increased with burning (1.23% unburned, 5.66% mild fire, 5.48% heavy fire); (3) The abundance of nitrogen-fixing nifH functional genes decreased with increasing fire intensity, whereas nitrification functional genes amoA-AOA and amoA-AOB exhibited the opposite trend. Light-intensity fires increased the abundance of denitrification functional genes nirK, nirS, and nosZ, while heavy fires reduced their abundance; (4) The correlation analysis demonstrated a strong association between soil bacteria and denitrification functional genes nifH and amoA-AOA, with soil total nitrogen being a key factor influencing the nitrogen cycle-related functional genes. The primary bacterial groups involved in soil nitrogen cycling were Proteobacteria, Actinobacteria, and Chloroflexi. These findings play a critical role in promoting vegetation regeneration and rapid ecosystem restoration in fire-affected areas. Full article
(This article belongs to the Section Forest Soil)
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22 pages, 3230 KiB  
Article
Study on Soil Nutrients and Microbial Community Diversity in Ancient Tea Plantations of China
by Jiaxin Li, Wei Huang, Xinyuan Lin, Waqar Khan, Hongbo Zhao, Binmei Sun, Shaoqun Liu and Peng Zheng
Agronomy 2025, 15(7), 1608; https://doi.org/10.3390/agronomy15071608 - 30 Jun 2025
Viewed by 235
Abstract
Ancient tea plantations possess extremely important economic and cultivation value. In China, ancient tea plantations with trees over 100 years old have been preserved. However, the status of soil microorganisms, soil fertility, and soil heavy metal pollution in these ancient tea plantations remains [...] Read more.
Ancient tea plantations possess extremely important economic and cultivation value. In China, ancient tea plantations with trees over 100 years old have been preserved. However, the status of soil microorganisms, soil fertility, and soil heavy metal pollution in these ancient tea plantations remains unclear. This study took four Dancong ancient tea plantations in Fenghuang, Chaozhou City, and Guangdong Province as the research objects. Soil samples were collected from the surface layer (0–20 cm) and subsurface layer (20–40 cm) of the ancient tea trees. The rhizosphere soil microbial diversity and soil nutrients were determined. On this basis, the soil fertility was evaluated by referring to the soil environmental quality standards so as to conduct a comprehensive evaluation of the soil in the Dancong ancient tea plantations. This study found that Proteobacteria, Acidobacteriota, Chloroflexi, and Actinobacteria were the dominant bacteria in the rhizosphere soil of the Dancong ancient tree tea plantation. Ascomycota and Mortierellomycota are the dominant fungal phyla. Subgroup_2, AD3, Acidothermus, and Acidibacter were the dominant bacterial genera. Saitozyma, Mortierella, and Fusarium are the dominant fungal genera. The redundancy analysis (RDA) revealed that at the bacterial phylum level, Verrucomicrobia showed positive correlations with alkali-hydrolyzable nitrogen (AN), available potassium (AK), and total nitrogen (TN); Proteobacteria exhibited a positive correlation with available phosphorus (AP); and Gemmatimonadetes was positively correlated with total potassium (TK). At the fungal phylum level, Ascomycota demonstrated a positive correlation with TK. TN, AN, and TK were identified as key physicochemical indicators influencing soil bacterial diversity, while TN, AN, AP, and AK were the key physicochemical indicators affecting soil fungal diversity. This study revealed that the soil of Dancong ancient tea plantations has reached Level I fertility in terms of TN, TP, SOM, and AP. TK and AN show Level I or near-Level I fertility, but AK only meets Level III fertility for tea planting, serving as the main limiting factor for soil fertility quality. Considering the relatively abundant TK content in the tea plantations, potassium-solubilizing bacteria should be prioritized over blind potassium fertilizer application. Meanwhile, it is particularly noteworthy that AN and SOM are at extremely high levels. Sustained excess of AN and SOM may lead to over-proliferation of dominant microorganisms, inhibition of other functional microbial communities, and disruption of ecological balance. Therefore, optimizing nutrient input methods during fertilization is recommended. Full article
(This article belongs to the Section Soil and Plant Nutrition)
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16 pages, 1110 KiB  
Article
Sustainable Treatment of High-Ammonia-Nitrogen Organic Wastewater via Anaerobic Ammonium Oxidation (Anammox) Combined with Effluent Recirculation/Micro-Aeration
by Zichun Yan, Rong Zeng and Hao Yang
Sustainability 2025, 17(13), 5926; https://doi.org/10.3390/su17135926 - 27 Jun 2025
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Abstract
High-ammonia-nitrogen organic wastewater poses significant challenges to traditional nitrogen removal processes due to their high energy consumption and carbon dependency, conflicting with global sustainability goals. Anammox presents a sustainable alternative with lower energy demands, yet its application is constrained by organic matter inhibition. [...] Read more.
High-ammonia-nitrogen organic wastewater poses significant challenges to traditional nitrogen removal processes due to their high energy consumption and carbon dependency, conflicting with global sustainability goals. Anammox presents a sustainable alternative with lower energy demands, yet its application is constrained by organic matter inhibition. This study aimed to optimize nitrogen and organic matter removal in Anammox systems by comparing two strategies: effluent recirculation and micro-aeration. Anammox reactors were operated under three conditions: (1) no recirculation (control group), (2) 100–300% effluent recirculation, (3) micro-aeration at 50–150 mL/min. The effects on total nitrogen (TN) and chemical oxygen demand (COD) removal were evaluated, alongside microbial community analysis via high-throughput sequencing. The results show that micro-aeration at 100 mL/min achieved 78.9% COD and 88.3% TN removal by creating micro-anaerobic conditions for metabolic synergy. Excessive aeration (150 mL/min) inhibited Anammox, dropping TN removal to 49.7%. Recirculation enriched Planctomycetota, while micro-aeration slightly increased Planctomycetota abundance at 45 cm and enhanced Proteobacteria and Chloroflexi for denitrification. Optimal conditions—200% recirculation and 100 mL/min aeration—improve efficiency via dilution and synergistic metabolism, providing a novel comparative framework for treating high-ammonia-nitrogen organic wastewater and filling a research gap in the parallel evaluation of Anammox enhancement strategies. Full article
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15 pages, 2036 KiB  
Article
Metagenomic Insights into How Understory Vegetation Enhances Soil Nitrogen Availability via Microbial Nitrogen Transformation in Poplar Plantations
by Wenyu Jia, Tong Li, Peilei Ye, Yuxin Chen, Ruoning Zhu, Ruixin Yan, Haoran Yue and Ye Tian
Agronomy 2025, 15(7), 1537; https://doi.org/10.3390/agronomy15071537 - 25 Jun 2025
Viewed by 335
Abstract
Long-term monoculture of poplar plantations for industrial material production has been widely reported to cause severe soil degradation, while the presence of understory vegetation might enhance soil nitrogen (N) transformation and supply. This study employed a field experiment using a randomized block design [...] Read more.
Long-term monoculture of poplar plantations for industrial material production has been widely reported to cause severe soil degradation, while the presence of understory vegetation might enhance soil nitrogen (N) transformation and supply. This study employed a field experiment using a randomized block design with three blocks and four understory treatments, including understory removal, N-fixing species planting, single-species retention, and diverse vegetation retention, in poplar plantations on a mid-latitude alluvial plain in China over 6 years to assess the effects of different species and richness of understory on soil N transformation and related microbial traits via 15N assays and shotgun metagenomics. The results showed that understory removal significantly reduced soil N transformation rates, bacterial abundance, and gene abundance associated with N transformation. Compared to a single-species understory, retaining a diverse understory with high species richness significantly increased soil gross N transformation rate of mineralization by 149%, nitrification by 221%, and immobilization by 85%; comprehensively enriched dominant bacterial phyla; and elevated gene abundances of gdh_K15371, ureB, hao, and amoA_B associated with N transformation. No significant difference in N transformation rates existed between N-fixing species planting treatment and single-species retention treatment, while N-fixing species planting treatment specifically promoted the soil bacterial phyla Nitrospirae and Chloroflexi, and increased the gene abundances of gdh_K15371 and hao. These findings demonstrate that both introducing N-fixing species and an increase in species richness of the understory effectively promoted soil N transformation but that different underlying mechanisms existed. Planting N-fixing species selectively increased the soil bacterial phyla of Nitrospirae and Chloroflexi, whereas the increase in species richness broadly enriched soil bacterial diversity, thereby inducing the enrichment of the functional genes and enhancing soil N transformation. In conclusion, both planting N-fixing species and retaining diverse understory vegetation were effective strategies for maintaining sustainable management of poplar plantations by increasing soil N availability. Full article
(This article belongs to the Section Soil and Plant Nutrition)
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17 pages, 1435 KiB  
Article
Effects of Cyclic Adenosine Monophosphate Nanoliposomes on Growth Performance, Gut Development and Microbiota of Broilers
by Li Chen, Li Wang, Sheng Huang, Guoqi Su, Shan Jiang, Feiyun Yang and Jingxiu Huang
Animals 2025, 15(13), 1852; https://doi.org/10.3390/ani15131852 - 23 Jun 2025
Viewed by 293
Abstract
This study aimed to investigate the effects of Nano-cAMP on growth performance, gut development, and microbiota composition in broilers. A total of 108 21-day-old yellow-feathered female chicks were randomly divided into three groups with six replicates per group and six chicks per replicate [...] Read more.
This study aimed to investigate the effects of Nano-cAMP on growth performance, gut development, and microbiota composition in broilers. A total of 108 21-day-old yellow-feathered female chicks were randomly divided into three groups with six replicates per group and six chicks per replicate according to the principle of consistent body weight. Experimental treatments included the following: (1) CON group (basal diet), (2) cAMP group (basal diet + 0.02 g/kg cAMP), and (3) Nano-cAMP group (basal diet + 0.37 g/kg Nano-cAMP liposomes). After a 21-day experimental period, results revealed the following: Compared with the CON group, the Nano-cAMP group exhibited a significantly reduced feed-to-gain ratio (p < 0.05). The cAMP group exhibited a significant increase in duodenal index (p < 0.05), whereas the Nano-cAMP group demonstrated greater jejunal villus height (p < 0.05). Both treatment groups showed significant upregulation of cholecystokinin (CCK) and secretin gene expression (p < 0.05). Analysis of alpha-diversity indices (Chao1, Shannon, Simpson) revealed no significant differences in jejunal and cecal microbiota composition between experimental groups (p > 0.05). Notably, the relative abundance of Firmicutes significantly increased (p < 0.05) in the cAMP and Nano-cAMP groups, whereas Proteobacteria, Gemmatimonadota, and Chloroflexi significantly decreased (p< 0.05). The combined relative abundance of three Lactobacillus genera and Bifidobacterium was obviously elevated. Linear discriminant analysis identified Bifidobacterium, Ruminococcus torques group, and uncultured_Thermoanaerobacterales_bacterium as dominant genera in the intestinal tract of Nano-cAMP group. In conclusion, dietary addition of Nano-cAMP promotes jejunal development, modulates appetite hormones mRNA expression, enhances absorption capacity, increases the relative abundance of intestinal probiotics such as Bifidobacterium and cellulose-degrading bacteria such as Ruminococcus torques group, optimizes gut microbiota composition, and ultimately reduces the feed-to-gain ratio in broilers. Full article
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