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Agronomy
Special Issues
Microbial Interactions and Functions in Agricultural Ecosystems
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Microbial Interactions and Functions in Agricultural Ecosystems

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Soil and Plant Nutrition".

Deadline for manuscript submissions: closed (25 February 2026) | Viewed by 4090

Special Issue Editors

Dr. Tanvi Govil

E-Mail Website
Guest Editor
Karen M Swindler Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA
Interests: biodegradation and bioremediation; sustainable biomanufacturing; environmental microbiology
Dr. Daniel Owens

E-Mail Website
Guest Editor
Department of Chemistry Biology and Health Sciences, South Dakota School of Mines & Technology, South Dakota Mines, Rapid City, SD 57701, USA
Interests: plant biochemistry; metabolic engineering
Special Issues, Collections and Topics in MDPI journals
Dr. Heidi Sieverding

E-Mail Website
Guest Editor
Department of Civil and Environmental Engineering, South Dakota School of Mines and Technology, Rapid City, SD, USA
Interests: life cycle analysis; Sustainability; greenhouse gas (GHG) footprint; environmental remediation; geohydrology; geospatial analysis

Special Issue Information

Dear Colleagues,

Soil health is crucial to crop production, but it was not until the 20th century that scientists began to uncover the complex interactions between soil microbes and plant roots. The rhizosphere, influenced by root secretions, is where these interactions are most intense. Today, the study of these interactions is more crucial than ever, especially in the context of climate change and sustainable agriculture. With the advancements in multi-omics technologies, our ability to decode this complex web of relationships between plants and their associated microbial communities has expanded. This Special Issue in Agronomy, titled “Microbial Interactions and Functions in Agricultural Ecosystems,” will focus on the following topics:

  • Exploring the contributions of soil and rhizosphere microbes to nutrient dynamics, soil structure, and plant health;
  • Examining how climate change, synthetic materials, and agricultural practices alter microbial community functions;
  • Decoding the complex interactions between plants and microbes using multi-omics technologies and simulation modeling;
  • Developing strategies to enhance microbial communities to improve crop productivity and sustainability.

Dr. Tanvi Govil
Dr. Daniel Owens
Dr. Heidi Sieverding
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

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 semimonthly 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

  • climate change
  • rhizosphere
  • root exudates
  • plant–microbe interactions
  • soil health
  • sustainable agriculture

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Published Papers (4 papers)

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Research

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22 pages, 5423 KB  
Article
Mechanisms of Diversified Crop Rotations in Alleviating Sunflower Continuous Cropping Obstacles Through Rhizosphere Microbiome Reconfiguration and Soil Enzymatic Activation
by Bing Yi, Dianxiu Song, Dexing Wang, Mingzhu Zhao, Xiaohong Liu, Yuxuan Cao, Jingang Liu and Liangshan Feng
Agronomy 2026, 16(7), 713; https://doi.org/10.3390/agronomy16070713 - 29 Mar 2026
Viewed by 529
Abstract
Sunflower (Helianthus annuus L.) production is severely hindered by continuous cropping obstacles, leading to soil degradation and significant yield declines. This study compared soybean–sunflower (G-H) and maize–sunflower (Z-H) rotations against sunflower monoculture (H-H) to elucidate the mechanisms of soil health restoration associated [...] Read more.
Sunflower (Helianthus annuus L.) production is severely hindered by continuous cropping obstacles, leading to soil degradation and significant yield declines. This study compared soybean–sunflower (G-H) and maize–sunflower (Z-H) rotations against sunflower monoculture (H-H) to elucidate the mechanisms of soil health restoration associated with crop rotation. Our results demonstrated that Z-H and G-H rotations led to a profound yield increase of 103.19% and 82.35%, respectively, with Z-H improving the 100-grain weight by 52.63%. Soil biological revitalization was evidenced by a 98.29% increase in sucrase activity and a 28.92% rise in alkaline phosphatase activity. Metagenomic analysis revealed that the rotation sequences increased bacterial Chao1 richness by 35.29% and fungal Shannon diversity by 20.17%. Specifically, the rotation treatments proactively recruited beneficial taxa such as Pontibacter (Log2FC > 3.0) and Panaeolus (Log2FC = 6.88), while effectively suppressing pathogens such as Ceratobasidiaceae. Co-occurrence network analysis identified a complex bacterial scaffold (199 nodes, 53 modules) that provided greater structural robustness than the fungal network (27 nodes). It is concluded that diversified rotations effectively mitigate continuous cropping obstacles by reactivating nutrient cycling and restructuring the rhizosphere into a stable, modular microbial interactome. This study provides a quantitative framework for utilizing biological strategies to restore soil health in degraded agroecosystems. Full article
(This article belongs to the Special Issue Microbial Interactions and Functions in Agricultural Ecosystems)
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20 pages, 2320 KB  
Article
Soil Physiochemical Property Variations and Microbial Community Response Patterns Under Continuous Cropping of Tree Peony
by Hao Pan, Min Zhu, Chenlong Ding and Junkang Wu
Agronomy 2025, 15(11), 2602; https://doi.org/10.3390/agronomy15112602 - 12 Nov 2025
Viewed by 764
Abstract
Continuous cropping can often deteriorate soil quality and reduce crop yield. Soil properties and microbial communities usually play a vital role in maintaining rhizosphere micro-ecosystem sustainability, which is yet to be addressed in continuous peony monoculture systems. Herein, variations in soil physiochemical properties [...] Read more.
Continuous cropping can often deteriorate soil quality and reduce crop yield. Soil properties and microbial communities usually play a vital role in maintaining rhizosphere micro-ecosystem sustainability, which is yet to be addressed in continuous peony monoculture systems. Herein, variations in soil physiochemical properties were extensively investigated following 1, 4, and 10 years of continuous tree peony cropping, as well as microbial community diversity, composition, and predicted functions. The soil pH and contents of available Mg, Mn, Zn, and B significantly declined after 10 years of continuous monoculture, while the contents of soil organic carbon, nitrate, and available P, K, Fe, and Cu notably increased by more than 100%, implying an imbalance of soil nutrients resulting from long-term continuous cropping. High-throughput sequencing results indicated that the microbial community structure and composition were remarkably altered after either 4 or 10 years of continuous cropping, interfering with diverse microbial metabolic pathways and phenotype functions. In addition, the relative abundances of some beneficial bacteria dramatically increased, especially for Acidobacteriota and Bacillus members. Microbial selections or adaptations in response to soil nutrient changes were expected to remediate negative impacts of continuous cropping on soil quality. Findings in this study provide insights into the establishment of proper management strategies for sustaining soil quality to resist potential obstacles after long-term continuous peony cropping. Full article
(This article belongs to the Special Issue Microbial Interactions and Functions in Agricultural Ecosystems)
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19 pages, 5884 KB  
Article
Partitioned Recirculating Renovation for Traditional Rice–Fish Farming Induced Substantial Alterations in Bacterial Communities Within Paddy Soil
by Yiran Hou, Hongwei Li, Rui Jia, Linjun Zhou, Bing Li and Jian Zhu
Agronomy 2025, 15(7), 1636; https://doi.org/10.3390/agronomy15071636 - 4 Jul 2025
Viewed by 1143
Abstract
Integrated agriculture–aquaculture (IAA), represented by integrated rice–fish farming, offers a sustainable production method that addresses global food issues and ensures food security. Partitioned recirculating renovation based on traditional integrated rice–fish farming is an effective way to facilitate the convenient harvesting of aquatic products [...] Read more.
Integrated agriculture–aquaculture (IAA), represented by integrated rice–fish farming, offers a sustainable production method that addresses global food issues and ensures food security. Partitioned recirculating renovation based on traditional integrated rice–fish farming is an effective way to facilitate the convenient harvesting of aquatic products and avoid difficulties associated with mechanical operations. To elucidate the impact of partitioned recirculating renovation on the bacterial communities within paddy field ecosystems, we investigated the soil environmental conditions and soil bacterial communities within integrated rice–fish farming, comparing those with and without partitioned recirculating renovations. The findings indicated a significant reduction in the bacterial community richness within paddy soil in the ditch (fish farming area), along with noticeable changes in the relative proportions of the predominant bacterial phyla in both the ditch and the rice cultivation area following the implementation of partitioned recirculating renovation. In both the ditch and the rice cultivation area, partitioned recirculating renovation diminished the edges and nodes in the co-occurrence networks for soil bacterial communities and considerably lowered the robustness index, negatively impacting the stability of bacterial communities in paddy soil. Simultaneously, the partitioned recirculating renovation substantially influenced the bacterial community assembly process, enhancing the relative contributions of stochastic processes such as dispersal limitation, drift, and homogenizing dispersal. In addition, partitioned recirculating renovation significantly altered the soil environmental conditions in both the ditch and the rice cultivation area, with environmental factors being markedly correlated with the soil bacterial community, especially the total nitrogen (TN) and total phosphorus (TP), which emerged as the primary environmental drivers influencing the soil bacterial community. Overall, these results elucidated the ecological impacts of partitioned recirculating renovation on the paddy soil from a microbiomic perspective, providing a microbial basis for optimizing partitioned rice–fish systems. Full article
(This article belongs to the Special Issue Microbial Interactions and Functions in Agricultural Ecosystems)
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Review

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35 pages, 11935 KB  
Review
In-Depth Insights into the Complex Interplay Between Microbial Diversity, Ecological Functionality, and Soil Health in Rice Agroecosystems
by Maria Alexandra Cucu and Elisa Zampieri
Agronomy 2026, 16(6), 595; https://doi.org/10.3390/agronomy16060595 - 10 Mar 2026
Viewed by 899
Abstract
Although microbial communities in rice agroecosystems regulate nitrogen transformations, methane dynamics, crop residue decomposition, and pathogen suppression, their integration into agronomic decision-making remains limited. Existing rice microbiome reviews largely describe taxonomic diversity without critically linking microbial processes to management trade-offs, greenhouse gas mitigation, [...] Read more.
Although microbial communities in rice agroecosystems regulate nitrogen transformations, methane dynamics, crop residue decomposition, and pathogen suppression, their integration into agronomic decision-making remains limited. Existing rice microbiome reviews largely describe taxonomic diversity without critically linking microbial processes to management trade-offs, greenhouse gas mitigation, and productivity outcomes. This review synthesizes current knowledge through a process-based and management-oriented framework, emphasizing how water and crop residue management, fertilization, tillage, and genotype selection shape microbial functionality rather than merely community composition. Advances in stable isotope probing (SIP), metatranscriptomics, and multi-omics have improved functional inference, yet a persistent gap remains between genetic potential and in situ process rates. By integrating microbiome science within a One Health perspective, we propose a conceptual framework linking microbial network structure to interconnected dimensions of ecosystem, plant, and human health. This framework addresses not only agronomic outcomes but also food safety concerns, including mycotoxin contamination by fungal pathogens, microbial contributions to nutritional quality, and pathways through which soil and plant microbiomes influence human health via the food chain. We critically examine how microbiome management can simultaneously target productivity, environmental sustainability, and health risk mitigation. We identify priority research needs in predictive microbial ecology, activity-based validation, and microbiome-informed management strategies. Rather than framing microbiomes as a universal solution to global food security, this review critically examines their realistic and context-dependent contribution to improving sustainability, resilience, and resource-use efficiency in rice production under climatic and environmental constraints, while safeguarding food safety and public health. Full article
(This article belongs to the Special Issue Microbial Interactions and Functions in Agricultural Ecosystems)
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