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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 3392

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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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

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 (3 papers)

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Research

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 181
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 1 | Viewed by 1156
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 1480
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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