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

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

Deadline for manuscript submissions: closed (31 December 2025) | Viewed by 38162

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Dr. Hui Wei

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Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
Interests: soil acidification; carbon cycle; soil health; global change
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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

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Keywords

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

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Published Papers (9 papers)

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Research

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17 pages, 3091 KB

Open AccessArticle

Chlorella vulgaris Enhances Soil Aggregate Stability in Rice Paddy Fields and Arable Land Through Alterations in Soil Extracellular Polymeric Substances

by Shaoqiang Huang, Xinyu Jiang, Hao Liu, Hongtao Jiang, Jiong Cheng, Heng Jiang, Shiqin Yu and Sanxiong Chen

Agronomy 2026, 16(2), 239; https://doi.org/10.3390/agronomy16020239 - 20 Jan 2026

Viewed by 409

Abstract

Microalgal amendments can improve soil structure by regulating extracellular polymeric substances (EPSs). However, the mechanisms underlying this process in red soils (characterized by high clay content and susceptibility to acidification) under different farming practices remain unclear. This study examined how Chlorella vulgaris (C. vulgaris) amendment influences EPS composition to enhance soil aggregate stability under arable land and rice paddy farming. A five-month pot experiment using a completely randomized design was conducted to investigate the effects of Chlorella vulgaris amendment on soils cultivated with Pennisetum × sinese and rice, two economically important crops commonly grown in South China. At the end of the experiment, Chlorella vulgaris amendment substantially increased both the mean weight diameter (MWD) and geometric mean diameter (GMD) of soil aggregates under both farming systems. Excitation–emission matrix (EEM) fluorescence spectroscopy revealed distinct changes in soil EPS components between the two farming types. Under arable land farming, humic-like and protein-like EPSs were dominant in Chlorella vulgaris-amended treatments, with fluorescence intensities more than doubling compared to the control. Conversely, under rice paddy farming, soil fulvic acid was the main component and showed a moderate increase. Partial least squares path modeling (PLS-PM) demonstrated that protein-like and humic-like EPSs had the strongest direct effects on aggregate stability in arable land red soil, while fulvic acid was the key factor in rice paddy red soil. The present study demonstrates that Chlorella vulgaris amendment improves aggregate stability in red soils through farming-specific, EPS-mediated pathways, providing a quantitative framework for researchers and land managers seeking to apply microalgal amendments for red soil enhancement and sustainable land management. 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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22 pages, 4687 KB

Open AccessArticle

Effects of Microbial Fertilizer on Soil Physicochemical Properties and Fungal Community Diversity in Saline–Alkali Soil Cultivated with Oil Sunflowers

by Shangqi Guan, Yantao Liu, Wei Duan, Kaiyong Wang, Peng Wang, Shengli Liu, Xiuping Jia and Yutong Hu

Agronomy 2025, 15(12), 2769; https://doi.org/10.3390/agronomy15122769 - 30 Nov 2025

Cited by 2 | Viewed by 946

Abstract

Soil salinization poses a significant threat to agricultural sustainability. This study investigated the effects of different microbial fertilizers on the rhizosphere fungal community and physicochemical properties of saline–alkali soil cultivated with sunflower. Three microbial fertilizers were applied at three concentration gradients to two sunflower varieties with contrasting salt–alkali tolerance (salt-tolerant NX53177 and salt-sensitive NKY1502) to elucidate the mechanisms underlying microbial fertilizer-mediated amelioration of saline–alkali soils. Among all treatments, the application of Aikesa microbial fertilizer at 50 g per pot (treatments T8 and T17) demonstrated the most pronounced ameliorative effects. In the salt-tolerant variety NX53177, the 50 g/L Aikesa fertilizer treatment increased the relative abundance of the beneficial genus Mortierella by 46.2%. It decreased the potentially pathogenic genus Lophotrichus by 82.2% compared to the no-fertilizer control. Soil fungal diversity was significantly improved, with the Shannon index increasing by 9.86% and the Simpson index decreasing by 25.83%. Concurrently, critical soil properties were enhanced: soil pH decreased by 7.79%, salinity decreased by 3.13%, and the contents of organic matter, available nitrogen, available phosphorus, and available potassium increased by 42.13%, 49.96%, 12.34%, and 53.22%, respectively. In the salt-sensitive variety NKY1502, the 50 g/L Aikesa fertilizer treatment increased Mortierella abundance by 15.96% and decreased Lophotrichus by 73.6% compared to the no-fertilizer control. The ACE and Shannon diversity indices increased by 10.00% and 9.92%, respectively, while the Simpson index decreased by 12.17%. Soil health was also markedly improved, with pH decreasing by 7.47%, salinity by 2.95%, and substantial increases in organic matter (57.94%), available nitrogen (75.78%), available phosphorus (13.20%), and available potassium (52.97%). In conclusion, the 50 g/L Aikesa fertilizer treatment effectively improved the rhizosphere fungal community structure and significantly enhanced soil physicochemical properties under saline–alkali stress. These findings provide a theoretical foundation and practical guidance for utilizing microbial fertilizers in ecological restoration and sustainable agricultural development of saline–alkali lands. 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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16 pages, 4046 KB

Open AccessArticle

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

Cited by 3 | Viewed by 2193

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 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 KB

Open AccessArticle

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

Cited by 2 | Viewed by 1509

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 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 KB

Open AccessArticle

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 8 | Viewed by 3543

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 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 KB

Open AccessArticle

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

Cited by 12 | Viewed by 3494

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 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 KB

Open AccessReview

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

Cited by 28 | Viewed by 13400

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 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 KB

Open AccessReview

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

Cited by 10 | Viewed by 3353

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. 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 KB

Open AccessReview

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 22 | Viewed by 7584

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, 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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