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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: 30 September 2025 | Viewed by 786

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 100 words) can be sent to the Editorial Office for announcement on this website.

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

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

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Published Papers (1 paper)

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Research

19 pages, 5884 KiB  
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 435
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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