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Agronomy
Special Issues
Soil Microbiomes and Their Roles in Soil Health and Fertility
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Soil Microbiomes and Their Roles in Soil Health and Fertility

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 September 2025) | Viewed by 3224

Special Issue Editor

Dr. José Manuel Meriles

E-Mail Website
Guest Editor
Instituto Multidisciplinario de Biología Vegetal (IMBIV-CONICET-UNC), Córdoba 5000, Argentina
Interests: land use change; desertification; land-use management; land degradation; sustainable development; soil chemistry; organic matter; land use; tillage systems; soil microbial community structure; soil enzymes; soil microbiology; high-throughput sequencing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue aims to advance the understanding of soil microbiology, plant–soil interactions, and biochemical processes that regulate soil functions and ecosystem dynamics. Emphasizing interdisciplinary approaches, it welcomes original manuscripts exploring the role of soil microorganisms in nutrient cycling, soil health, agricultural sustainability, and ecosystem services.

Key topics include the ecology of soil microorganisms, plant–soil relationships, and the interactions between soil microbiome, physical properties, and chemical properties. Studies applying innovative molecular, microscopic, and analytical techniques to soil microbiota dynamics are highly valued. Manuscripts should address mechanistic insights, integrating soil microbiology, plant nutrition, agronomy, mineral fertilizers, organic amendments, and environmental sciences, particularly in human-managed and semi-natural systems.

The journal prioritizes research that bridges fundamental discoveries with practical applications, enhancing sustainability and resilience in agricultural and natural systems while providing novel perspectives on soil ecosystem functions. Interdisciplinary and groundbreaking contributions are especially encouraged.

Dr. José Manuel Meriles
Guest Editor

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

  • soil microbiology
  • plant–soil interactions
  • soil microbiome
  • sustainability
  • ecosystem services

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Published Papers (3 papers)

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Research

16 pages, 2204 KB  
Article
Three Pineapple Root VOCs Affect Soil Health via Microbial Changes in Banana Rhizosphere
by Xinyue Chen, Yunfeng Lu, Taisheng Jiang, Peize Li, Xiaoqiang Deng, Jinming Yang, Beibei Wang and Rong Li
Agronomy 2025, 15(11), 2520; https://doi.org/10.3390/agronomy15112520 - 29 Oct 2025
Viewed by 611
Abstract
Soil-borne diseases of banana severely threaten the sustainable development of the banana industry. In the pineapple–banana rotation system, using rhizosphere microorganisms to control banana Fusarium wilt via pineapple root exudates is a promising green control strategy. However, the role of volatile organic compounds [...] Read more.
Soil-borne diseases of banana severely threaten the sustainable development of the banana industry. In the pineapple–banana rotation system, using rhizosphere microorganisms to control banana Fusarium wilt via pineapple root exudates is a promising green control strategy. However, the role of volatile organic compounds (VOCs) in mediating disease suppression remains unclear. To explore the disease-inhibiting mechanisms, this study employed in vitro assays and high-throughput sequencing to evaluate the effects of three pineapple-root-derived VOCs (decanal, nonanal, octanol). The results showed the following: (1) All three VOCs strongly inhibited the mycelial growth of Fusarium, with octanol exhibiting the highest inhibition. (2) Each VOC promoted Arabidopsis thaliana growth, and decanal was the most effective. (3) In pot experiments, these VOCs significantly altered the banana rhizosphere microbial community, facilitating the colonization of beneficial genera—characterized by reduced microbial diversity and increased beneficial genera abundance. These results delineate a VOC-mediated rhizosphere microbe–Fusarium–plant interaction network, offering a novel theoretical foundation for the ecological control of banana diseases via the rhizosphere microbiome. In conclusion, this study elucidates a new mechanism for banana disease inhibition via VOCs, highlighting the positive impacts on plant growth and rhizosphere soil health through microbiota modulation. Full article
(This article belongs to the Special Issue Soil Microbiomes and Their Roles in Soil Health and Fertility)
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21 pages, 5076 KB  
Article
Exploring Organic Matter, Soil Enzymes, and Fungal Communities Under Land-Use Intensification in the Argentine Pampas
by Florencia M. Barbero, Romina A. Verdenelli, María F. Dominchin, Ileana Frasier, Silvina B. Restovich, Dannae L. Serri, Ernesto J. Campilongo-Mancilla, Valeria S. Faggioli, Ana G. Iriarte, Silvina Vargas-Gil and José M. Meriles
Agronomy 2025, 15(11), 2469; https://doi.org/10.3390/agronomy15112469 - 24 Oct 2025
Cited by 1 | Viewed by 853
Abstract
Intensive land use in the Argentine Pampas has led to soil degradation, yet links between soil organic matter (SOM) composition, enzyme activity, and fungal communities remain unclear. This study compared contrasting ecoregions and land uses: pristine (PI), pasture (PA), crop rotation with cover [...] Read more.
Intensive land use in the Argentine Pampas has led to soil degradation, yet links between soil organic matter (SOM) composition, enzyme activity, and fungal communities remain unclear. This study compared contrasting ecoregions and land uses: pristine (PI), pasture (PA), crop rotation with cover crops (RO), and monoculture (MO). Infrared spectra showed that PI soils in Anguil had higher absorbance in hydroxyl/amine (3400 cm−1: 0.90 ± 0.08) and carbonyl (1750 cm−1: 0.52 ± 0.12) bands than MO soils (0.47 ± 0.30 and 0.35 ± 0.06; p < 0.05), indicating greater SOM diversity. Pergamino soils showed smaller differences, reflecting site-specific effects. Enzyme activities also responded to land use. In Anguil, xylosidase, β-1,4-N-acetylglucosaminidase, and phosphatase peaked under PI (40, 127, and 443 nmol g−1 h−1). In Pergamino, xylosidase and β-1,4-N-acetylglucosaminidase were higher under PA and PI, indicating enhanced microbial functionality under low disturbance. Fungal composition varied with land use and location: Mortierellomycetes dominated in Pergamino, while Leotiomycetes and Agaricomycetes were more abundant in PI and PA, and Dothideomycetes increased in MO and RO. Despite compositional shifts, fungal diversity changed little. Integrating chemical, biochemical, and molecular indicators revealed how land-use intensification modifies SOM and microbial processes in Pampas soils. Full article
(This article belongs to the Special Issue Soil Microbiomes and Their Roles in Soil Health and Fertility)
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18 pages, 4366 KB  
Article
Microbiome Analysis of Rhizosphere Soil of Wild Succulent Shrubs Zygophyllum coccineum and Haloxylon salicornicum
by Abdulaziz Alharbi and Medhat Rehan
Agronomy 2025, 15(3), 717; https://doi.org/10.3390/agronomy15030717 - 16 Mar 2025
Cited by 1 | Viewed by 1244
Abstract
Zygophyllum coccineum L. and Haloxylon salicornicum are dominant plant species in the natural habitats of Saudi Arabia. The soil microbiome is indispensable for nutrient cycling and stress resilience. In the present study, the analysis of soil nutrients under the two plants displayed variable [...] Read more.
Zygophyllum coccineum L. and Haloxylon salicornicum are dominant plant species in the natural habitats of Saudi Arabia. The soil microbiome is indispensable for nutrient cycling and stress resilience. In the present study, the analysis of soil nutrients under the two plants displayed variable differences in total N, K, Zn, Mn and Cu, with significant differences in both K and Mn (p ≤ 0.05). In general, the available soil nutrients were higher under Haloxylon than Zygophyllum plants, reflecting higher N, K, Fe and Cu contents in the leaves of the Haloxylon plant. Metagenomic analysis of soil microbiome revealed that the top abundant bacteria at the phylum level were Actinobacteriota, Chloroflexi and Proteobacteria, whereas the uppermost fungal communities were Ascomycota, followed by Basidiomycota. The predicted abundant enzymes in the bacterial communities included Phosphoadenylyl-sulfate reductase, Serine-type D-Ala-carboxypeptidase, ADP-glyceromanno-heptose 6-epimerase and glutathione hydrolase. The fungal communities associated with Haloxylon possessed more than 48 enzymes that differed in their richness from the communities of Zygophyllum. Pentose-P and Sulphate-Cys pathways disclosed the extreme abundant pathways in Zygophyllum bacterial communities, while the nonoxipent pathway was overabundant in the Haloxylon fungal communities. While genomic predictions provide insights into functional potential, integrating these data with environmental parameters remains key to managing soil health. Full article
(This article belongs to the Special Issue Soil Microbiomes and Their Roles in Soil Health and Fertility)
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