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Agronomy
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Effects of the Soil Microbiome on Nutrient Cycling and Soil...
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Effects of the Soil Microbiome on Nutrient Cycling and Soil Health in Agroecosystems

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Agroecology Innovation: Achieving System Resilience".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 8411

Special Issue Editor

Dr. Hui Wei

E-Mail Website
Guest Editor
Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
Interests: soil ecology; soil carbon and nitrogen cycle; soil remediation

Special Issue Information

Dear Colleagues,

Soil microbiomes consist of a diverse community of microorganisms, including bacteria, fungi, and other groups, which interact to influence nutrient availability to plants, decompose soil organic matter, and form soil structure. These interactions are essential for the cycling of nutrients, such as nitrogen, phosphorus, and potassium, which are essential for plant growth and productivity. Therefore, the soil microbiome plays a critical role in driving nutrient cycling and maintaining soil health in agroecosystems. In agroecosystems, the composition and activity of the soil microbiome could be influenced by agricultural practices and management, such as tillage, fertilization, and crop rotation. Understanding the effects of these practices on the soil microbiome is critical in order to maintain sustainable agricultural development and ensure food safety. This Special Issue intends to collect and publish research advances on the effects of the soil microbiome on nutrient cycling and soil health in agroecosystems, which appears to be a highly attractive topic and well within the scope of agronomy.

Dr. Hui Wei
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • soil biodiversity
  • soil food web
  • soil microbiomes
  • soil health
  • nutrient cycling
  • agricultural practices
  • agroecosystems

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Published Papers (7 papers)

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Research

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16 pages, 4046 KiB  
Article
Effects of Continuous Return of Bt Corn Straw on Soil Nutrients, Enzyme Activities, and Microbial Communities
by Chenning Zhang, Xiao Lv, Xiaomin Liang, Peng Peng and Yuanjiao Feng
Agronomy 2024, 14(11), 2737; https://doi.org/10.3390/agronomy14112737 - 20 Nov 2024
Viewed by 629
Abstract
The impact of Bacillus thuringiensis (Bt) corn straw returning on the soil ecosystem has attracted significant attention. In this study, taking the homologous conventional corn 5422 as a control, we explored the effects of Bt corn (5422Bt1 and 5422CBCL) straw return after five [...] Read more.
The impact of Bacillus thuringiensis (Bt) corn straw returning on the soil ecosystem has attracted significant attention. In this study, taking the homologous conventional corn 5422 as a control, we explored the effects of Bt corn (5422Bt1 and 5422CBCL) straw return after five consecutive cycles on soil nutrients, enzyme activities, and microbial communities. The results showed that in the 5422Bt1 treatment, the levels of available phosphorus (AP), total nitrogen (TN), and sucrose enzyme (SUC) activities significantly increased. In the 5422CBCL treatment, organic matter (OM), alkaline nitrogen (AN), and AP contents, as well as SUC and acid phosphatase (ACP) activities, significantly decreased, while available potassium (AK) and TN contents significantly increased. Through Illumina high-throughput sequencing, it was found that the OTU abundance of soil fungi and bacteria changed after straw returning, and there were no significant differences in alpha diversity (α-diversity) among the three treatments. Redundancy analysis (RDA) indicated that soil nutrients and enzyme activities also affect the soil microbial communities. In summary, Bt corn straw returning affects soil nutrients, enzyme activities, and the structure of microbial communities. Overall, this study revealed the impact of continuous Bt corn straw returning on the soil ecosystem, providing a theoretical basis for subsequent studies. Full article
(This article belongs to the Special Issue Effects of the Soil Microbiome on Nutrient Cycling and Soil Health in Agroecosystems)
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14 pages, 840 KiB  
Article
Soil Biocrusts May Exert a Legacy Impact on the Rhizosphere Microbial Community of Plant Crops
by Xiangbo Zou, Xinyu Jiang, Heng Jiang, Cheng Li, Jiong Cheng, Dongqing Ji, Jin Wang, Jiajin Ruan, Tiancheng Zhou, Cao Kuang, Ji Ye and Shiqin Yu
Agronomy 2024, 14(11), 2548; https://doi.org/10.3390/agronomy14112548 - 30 Oct 2024
Viewed by 586
Abstract
Biological soil crusts (biocrusts) play important ecological roles in many ecosystems, but their legacy effects in subtropical agricultural systems are poorly understood. This study investigated how biocrusts impact soil properties and subsequent crop rhizosphere microbiomes. Soil with (+BC) and without (−BC) biocrusts was [...] Read more.
Biological soil crusts (biocrusts) play important ecological roles in many ecosystems, but their legacy effects in subtropical agricultural systems are poorly understood. This study investigated how biocrusts impact soil properties and subsequent crop rhizosphere microbiomes. Soil with (+BC) and without (−BC) biocrusts was cultivated and used to grow pepper plants in a greenhouse experiment. Soil physicochemical properties and microbial communities in the pre-planting soils, and microbial communities in crop rhizosphere were analyzed. The results showed that soils with biocrust had significantly higher organic matter, total nitrogen, alkaline hydrolyzable nitrogen, total phosphorus, and total potassium content. Microbial community structures differed significantly among treatments, with −BC soils exhibiting higher microbial diversity in pre-planting conditions, while +BC soils showed higher diversity in crop rhizosphere soils. Soil properties, especially extractable potassium, total nitrogen, and organic matter content, were significantly correlated with rhizosphere microbial community structure. Additionally, our results showed that the first principal coordinate (PCoA1) of soil microbial community structure was significantly correlated with rhizosphere microbiota. Multiple regression analysis revealed that pre-planting soil microbial diversity indices and certain soil physicochemical properties could predict crop rhizosphere soil microbial diversity. Our results demonstrate that biocrusts can enhance soil fertility and alter microbial communities in subtropical agricultural soils, with persistent effects on the crop rhizosphere microbiome. This study provides new insights into the ecological legacy of biocrusts in managed subtropical ecosystems and their potential agricultural implications. Full article
(This article belongs to the Special Issue Effects of the Soil Microbiome on Nutrient Cycling and Soil Health in Agroecosystems)
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28 pages, 3960 KiB  
Article
Effect of Mineral Fertilizers and Pesticides Application on Bacterial Community and Antibiotic-Resistance Genes Distribution in Agricultural Soils
by Ludmila Khmelevtsova, Tatiana Azhogina, Shorena Karchava, Maria Klimova, Elena Polienko, Alla Litsevich, Elena Chernyshenko, Margarita Khammami, Ivan Sazykin and Marina Sazykina
Agronomy 2024, 14(5), 1021; https://doi.org/10.3390/agronomy14051021 - 11 May 2024
Cited by 3 | Viewed by 1643
Abstract
Soils are a hotspot for the emergence and spread of antibiotic resistance. The effects of agrochemical treatments on the bacterial community of agricultural soils and the content of antibiotic-resistance genes (ARGs) were studied. Treatments included the following: control, mineral fertilizers (NPKs), pesticides, and [...] Read more.
Soils are a hotspot for the emergence and spread of antibiotic resistance. The effects of agrochemical treatments on the bacterial community of agricultural soils and the content of antibiotic-resistance genes (ARGs) were studied. Treatments included the following: control, mineral fertilizers (NPKs), pesticides, and the combined treatment of soils under soya (Glycine max), sunflower (Helianthus annuus L.), and wheat (Triticum aestivum). Bacterial community taxonomic composition was studied using 16S rRNA gene sequencing. The content of 10 ARGs and 3 integron genes (intI1, intI2, intI3) was determined using quantitative real-time PCR. The results showed that the treatments had little effect on the taxonomic composition and diversity of the soil bacterial community. The most significant factors determining differences in the microbial community were sampling time and soil physico-chemical parameters. A significant role of the bacterial community in ARG distribution in soils was demonstrated. Representatives of the Pseudomonas, Bacillus, Sphingomonas, Arthrobacter genera, and the Nocardioidaceae and Micrococcaceae families were likely ARG hosts. The presence of integron genes of all three classes was detected, the most numerous being intI3. This work provides important information on the role of agricultural soils in ARG transfer, and the findings may be useful for sustainable and safe agricultural development. Full article
(This article belongs to the Special Issue Effects of the Soil Microbiome on Nutrient Cycling and Soil Health in Agroecosystems)
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15 pages, 3578 KiB  
Article
Nitric Acid Rain Decreases Soil Bacterial Diversity and Alters Bacterial Community Structure in Farmland Soils
by Xuan Chen, Yiming Wang, Hui Wei and Jiaen Zhang
Agronomy 2024, 14(5), 971; https://doi.org/10.3390/agronomy14050971 - 5 May 2024
Viewed by 1904
Abstract
Being regarded as one of the environmental problems endangering biodiversity and ecosystem health, acid rain has attracted wide attention. Here, we studied the effects of nitric acid rain (NAR) on the structure and diversity of microbial communities in agricultural soils by laboratory incubation [...] Read more.
Being regarded as one of the environmental problems endangering biodiversity and ecosystem health, acid rain has attracted wide attention. Here, we studied the effects of nitric acid rain (NAR) on the structure and diversity of microbial communities in agricultural soils by laboratory incubation experiments and greenhouse experiments. Our results indicated that NAR had an inhibitory effect on soil microorganisms, showing a significant reduction in the Chao1 index and Shannon index of soil bacteria. Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi were the dominant bacterial phyla under NAR stress in this study. NAR significantly reduced the relative abundance of Proteobacteria and Actinobacteria, but significantly increased the relative abundance of Acidobacteriota and Chloroflexi, suggesting that NAR was unfavorable to the survival of Proteobacteria, and Actinobacteria. It is worth noting that the inhibitory or promoting effect of NAR on the dominant bacterial phyla gradually increased with increasing NAR acidity and treatment time. In addition, the study observed that the change in soil pH caused by NAR was the main reason for the change in soil bacterial community structure. In summary, the effects of NAR on soil microorganisms cannot be underestimated from the perspective of sustainable agricultural development. Full article
(This article belongs to the Special Issue Effects of the Soil Microbiome on Nutrient Cycling and Soil Health in Agroecosystems)
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Review

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29 pages, 1040 KiB  
Review
Microbiological Indicators for Assessing the Effects of Agricultural Practices on Soil Health: A Review
by Mikhail V. Semenov, Alena D. Zhelezova, Natalya A. Ksenofontova, Ekaterina A. Ivanova, Dmitry A. Nikitin and Vyacheslav M. Semenov
Agronomy 2025, 15(2), 335; https://doi.org/10.3390/agronomy15020335 - 28 Jan 2025
Viewed by 657
Abstract
Agricultural practices significantly impact soil properties and ecological functions, highlighting the importance of comprehensive soil health assessments. Traditionally, these assessments have focused on physical and chemical indicators, often neglecting microbiological properties. This review explores the potential of microbiological indicators in evaluating the effects [...] Read more.
Agricultural practices significantly impact soil properties and ecological functions, highlighting the importance of comprehensive soil health assessments. Traditionally, these assessments have focused on physical and chemical indicators, often neglecting microbiological properties. This review explores the potential of microbiological indicators in evaluating the effects of agricultural practices on soil ecological functions, emphasizing their significance and addressing challenges associated with their application. A key advantage of microbiological indicators is their high sensitivity and rapid response to environmental changes. These indicators can be grouped into three categories: microbial biomass and abundance, microbial taxonomic composition and diversity, and microbial activity. Among these, microbial biomass carbon, basal respiration, and decomposition rates are considered the most reliable and interpretable indicators. Microbial taxonomic composition and diversity remain limited in their diagnostic and predictive capabilities due to challenges in interpretation. Integrating microbiological indicators offers a more holistic understanding of the interactions between agricultural practices and soil health, enhancing our ability to monitor, manage, and preserve soil ecosystems. To facilitate their adoption in agricultural production and land management, further efforts are needed to improve the interpretability of these indicators and to establish standardized criteria for soil health assessment. Full article
(This article belongs to the Special Issue Effects of the Soil Microbiome on Nutrient Cycling and Soil Health in Agroecosystems)
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17 pages, 2539 KiB  
Review
Effects of Straw and Green Manure Addition on Crop Yield, Soil Properties and CH4 Emissions: A Meta-Analysis
by Qi Jia, Hongjun Zheng, Zhaoji Shi, Xing Liu, Daolin Sun and Jiaen Zhang
Agronomy 2024, 14(11), 2724; https://doi.org/10.3390/agronomy14112724 - 19 Nov 2024
Viewed by 759
Abstract
The incorporation of organic amendments is widely acknowledged for its capacity to enhance soil fertility and boost crop productivity. However, whether the addition of organic amendments can improve soil quality and crop production, simultaneously causing methane emissions in paddy fields, deserves further investigation. [...] Read more.
The incorporation of organic amendments is widely acknowledged for its capacity to enhance soil fertility and boost crop productivity. However, whether the addition of organic amendments can improve soil quality and crop production, simultaneously causing methane emissions in paddy fields, deserves further investigation. In this meta-analysis, the effects of different organic amendments on soil nutrient levels, rice yield and CH4 emissions were evaluated in paddy fields based on 328 observations from 77 field trial studies. Our results revealed that the addition of organic amendments significantly increased soil organic carbon (9.47%), microbial biomass carbon (21.13%), microbial biomass nitrogen (28.91%), urease (25.07%) and β-glucosidase (24.41%). Moreover, straw addition significantly increased the CH4 emissions by 152.68% and rice yield by 7.16%; green manure addition significantly increased CH4 emissions by 71.62% and rice yield by 10.09%, respectively. Although both increased the CH4 emissions, green manure had the ability to improve the availability of N, which could improve rice uptake. The regression results showed that the variation in crop yield, soil nutrients and CH4 emissions are influenced through the types and quality of organic amendments. Overall, this study suggests that organic amendments are beneficial in maintaining soil quality and improving rice yield, whereas it also increased the CH4 emissions. These meta-analysis results may provide some references for optimizing organic amendments incorporated into the soil to sustain soil fertility and crop production while mitigating soil constraints and methane emissions. Full article
(This article belongs to the Special Issue Effects of the Soil Microbiome on Nutrient Cycling and Soil Health in Agroecosystems)
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20 pages, 681 KiB  
Review
Effective Microbial Strategies to Remediate Contaminated Agricultural Soils and Conserve Functions
by Carolina E. Demaman Oro, Bruna M. Saorin Puton, Luciana D. Venquiaruto, Rogério M. Dallago and Marcus V. Tres
Agronomy 2024, 14(11), 2637; https://doi.org/10.3390/agronomy14112637 - 8 Nov 2024
Cited by 1 | Viewed by 1379
Abstract
The growing global emphasis on sustainable agriculture has brought increased attention to the health and productivity of soils, especially through the lens of soil microbiology. Microbial communities in soil are essential for nutrient cycling, organic matter decomposition, and maintaining overall soil health. However, [...] Read more.
The growing global emphasis on sustainable agriculture has brought increased attention to the health and productivity of soils, especially through the lens of soil microbiology. Microbial communities in soil are essential for nutrient cycling, organic matter decomposition, and maintaining overall soil health. However, agricultural practices, including synthetic fertilizers and intensive farming, have led to short time impacts in these microbial ecosystems, potentially threatening soil fertility and environmental quality. Agricultural expansion and food production generate waste and chemical inputs, such as heavy metals, pesticides, and herbicides, leading to significant environmental contamination. This scenario requires the implementation of remediation strategies that are both sustainable and energy efficient. In this context, microbiological processes present a much promising approach to mitigating the environmental impacts of soil pollution. Techniques such as bioremediation, which harness the natural metabolic capabilities of soil microorganisms, and bioaugmentation, which involves the introduction of specific microbial strains to increase degradation processes, are being explored. These approaches are vital for restoring soil health, contributing to environmental conservation and soil biodiversity, improving nutrient cycling, and promoting long-term agricultural productivity. Full article
(This article belongs to the Special Issue Effects of the Soil Microbiome on Nutrient Cycling and Soil Health in Agroecosystems)
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