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Soil Health and Plant Microbiome–Bioeffectors Relationship in Sustainable Agriculture, 2nd...
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Soil Health and Plant Microbiome–Bioeffectors Relationship in Sustainable Agriculture, 2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: 30 June 2026 | Viewed by 11981

Special Issue Editors

Prof. Dr. Nikolay Vassilev

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Guest Editor
Department of Chemical Engineering, and Institute of Biotechnology, Faculty of Sciences, University of Granada, c/Fuentenueva s/n, E-18071 Granada, Spain
Interests: industrial microbiology; bioreactors and fermentation processes; cell and enzyme immobilization; biotechnological production of enzymes, organic acids, biofuels; plant microbiome; plant-microbial interactions; microbial mineral dissolution; production and formulation of soil inoculants
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Stefan Shilev

E-Mail Website
Guest Editor
Department of Microbiology and Environmental Biotechnologies, Faculty of Plant Protection and Agroecology, Agricultural University – Plovdiv, 4000 Plovdiv, Bulgaria
Interests: soil microbiology; plant growth-promoting bacteria (PGPB); phytoremediation; biowaste composting and recycling
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Sustainable agriculture strives to meet the nutritional needs of the human population, combining this aspiration with the recovery and maintenance of soil fertility, natural resources, and environmental protection. Microbial communities are essential in managing plant and soil health to obtain increased crop yields with good quality. Microorganisms distributed in the rhizosphere, in plant tissues or on their surface, are prominently "selected" by the plants themselves through the habitat’s characteristics. The progress in agricultural practices and circular bioeconomy achieved in recent years, such as no-till, intermediate, and cover crops, green manure, soil organic amendments, crop rotations, and so on, also model the highly diverse microbial communities. Undoubtedly, the role of these communities is crucial, and in some cases decisive, for plant and soil health, crop resistance, and the mitigation of abiotic and biotic stressors, and thus also for the quantity and quality of crop production. In this regard, the focus of the present Special Issue of Microorganisms is the plant-associated microbiome as an essential piece of the puzzle named sustainable agriculture. The scope is broad and unrestrictive, referring to rhizosphere microbial communities, endophytes, etc. We aim to bring together and showcase original, novel studies and reviews on the plant-associated microbiome in sustainable agriculture. Studies on the beneficial microorganisms in sustainable agriculture are more than welcome.

Prof. Dr. Nikolay Vassilev
Prof. Dr. Stefan Shilev
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. Microorganisms 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 2700 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

  • plant-associated microbiome
  • plant–microbiome bioeffectors
  • microbial diversity
  • soil health
  • sustainable agriculture
  • circular bioeconomy

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Published Papers (5 papers)

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Research

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29 pages, 20703 KB  
Article
Habitat-Adapted Endophytic Fusarium clavum EeR24 from the Arava Desert Induces Resistance Against Fusarium Wilt of Muskmelons
by Vineet Meshram, Meirav Elazar, Marcel Maymon, Gunjan Sharma, Eduard Belausov, Dana Charuvi, Mahiti Gupta, Soniya Goyal, Surbhi Goel and Stanley Freeman
Microorganisms 2026, 14(4), 871; https://doi.org/10.3390/microorganisms14040871 - 12 Apr 2026
Viewed by 723
Abstract
Muskmelon (Cucumis melo) is a widely cultivated and economically important fruit crop that is severely affected by Fusarium wilt caused by Fusarium oxysporum f. sp. melonis (race 1.2) (Fom). Conventional management practices have shown limited effectiveness and pose environmental and health [...] Read more.
Muskmelon (Cucumis melo) is a widely cultivated and economically important fruit crop that is severely affected by Fusarium wilt caused by Fusarium oxysporum f. sp. melonis (race 1.2) (Fom). Conventional management practices have shown limited effectiveness and pose environmental and health risks; therefore, sustainable and eco-friendly alternatives are required to manage this disease. In the present study, 23 endophytic fungal isolates belonging to eight genera were isolated from Ecballium elaterium and screened to determine antifungal potential against Fom using an in vitro antagonistic assay. Two endophytic isolates (Fusarium sp. EeR4 and Fusarium clavum EeR24) exhibited an inhibitory effect against Fom on quarter-strength PDA plates. In growth chamber experiments, F. clavum EeR24-colonized melon seedlings and significantly protected plants from wilting compared to non-colonized pathogen-challenged seedlings. Under greenhouse conditions, F. clavum EeR24 significantly improved morphological and physiological traits, including plant height, weight, number of leaves, membrane stability, photosynthesis, stomatal conductance, and transpiration, in Cucumis melo. Endophytic colonization improved catalase (56%), guaiacol peroxide (47%), and superoxide dismutase activity (25%), and increased flavonoid and phenolic content by 11–59% compared to non-colonized Fom-challenged plants. Lipid peroxidation significantly decreased by 37% and proline accumulation increased by 70% in colonized plants compared to non-colonized plants. Histochemical analysis also indicated that endophytic colonization considerably reduced the levels of H2O2, O2−, malondialdehyde, and cell mortality in Fom-challenged plants. In addition, the culture filtrate and organic residues of F. clavum EeR24 inhibited the mycelial growth of Fom by 52–58%, respectively. Furthermore, a study on spatial colonization of the endophyte and the pathogen using GFP and RFP tagging indicated that both the endophyte and the pathogen simultaneously colonized the root tissues of C. melo; however, the endophyte significantly reduced the pathogenicity of Fom. These results suggest that endophytic F. clavum EeR24 may be developed as an effective biocontrol agent for the management of Fusarium wilt in melon plants under field conditions. Full article
(This article belongs to the Special Issue Soil Health and Plant Microbiome–Bioeffectors Relationship in Sustainable Agriculture, 2nd Edition)
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24 pages, 2819 KB  
Article
Long-Term Organic Fertilization Enhances Soil Fertility and Reshapes Microbial Community Structure with Decreasing Effects Across Soil Depth
by Suyao Li, Yulin Li, Xu Yan, Zhengyang Gu, Dong Xue, Kaihua Wang, Yuting Yang, Min Lv, Yujie Han, Jinbiao Li, Yanyan Lv and Anyong Hu
Microorganisms 2026, 14(1), 250; https://doi.org/10.3390/microorganisms14010250 - 21 Jan 2026
Cited by 1 | Viewed by 1280
Abstract
Sustaining agricultural productivity and soil health under intensive cultivation requires a comprehensive understanding of fertilization effects, particularly on deeper soil layers, which has received limited attention compared to surface soils. This study investigated how different fertilization regimes (inorganic, organic, and combined organic–inorganic fertilizers) [...] Read more.
Sustaining agricultural productivity and soil health under intensive cultivation requires a comprehensive understanding of fertilization effects, particularly on deeper soil layers, which has received limited attention compared to surface soils. This study investigated how different fertilization regimes (inorganic, organic, and combined organic–inorganic fertilizers) influence soil physicochemical properties, microbial diversity, community structure, and functional gene abundances at three soil depths (0–20 cm, 20–40 cm, and 40–60 cm) in a 40-year fertilization experiment. Organic fertilization significantly improved topsoil fertility indicators such as soil organic matter (56.6–109.2%), total nitrogen (66.7–122.0%), total phosphorus (198.6–413.2%), and available phosphorus (984.8–1622.1%) and potassium (35.3–438.1%). Compared with the unfertilized control and nitrogen-only treatment, rice yield increased by 97.1–130.5% under NPK and sole organic fertilization, and further increased by 184.1–255.9% under combined organic–inorganic fertilization. However, fertilization effects diminished with soil depth due to limited nutrient mobility. Microbial diversity significantly decreased with depth and was minimally influenced by fertilization treatments. Microbial community structure varied notably among fertilization treatments at the surface layer, mainly driven by soil nutrients, whereas soil depth had a dominant effect on microbial community structure and compositions. Co-occurrence networks showed the highest complexity in surface soil microbial communities, which declined with soil depth, reflecting potential synergistic and mutualistic relationships in topsoil and the adaptation of microbial communities to nutrient-limited conditions in subsoil. Microbial functional gene analyses highlighted clear depth-dependent distributions, with surface layers enriched in decomposition-related genes, while deeper layers favored anaerobic processes. Overall, long-term fertilization exerted strong depth-dependent effects on soil fertility, microbial community structure, and functional potential in paddy soils. Full article
(This article belongs to the Special Issue Soil Health and Plant Microbiome–Bioeffectors Relationship in Sustainable Agriculture, 2nd Edition)
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20 pages, 3802 KB  
Article
Metabarcoding Analysis of Rhizosphere and Bulk Soils in Bulgaria Reveals Fungal Community Shifts Under Oat–Vetch Intercropping Versus Sole Oat Cultivation
by Stefan Shilev, Mariana Petkova and Ivelina Neykova
Microorganisms 2026, 14(1), 42; https://doi.org/10.3390/microorganisms14010042 - 24 Dec 2025
Viewed by 679
Abstract
Fungal communities in the rhizosphere are crucial in maintaining soil health, driving nutrient cycling, and enhancing plant productivity. This study examined the role of intercropping of oats (Avena sativa L.) with vetch (Vicia sativa L.) and their subsequent use as green [...] Read more.
Fungal communities in the rhizosphere are crucial in maintaining soil health, driving nutrient cycling, and enhancing plant productivity. This study examined the role of intercropping of oats (Avena sativa L.) with vetch (Vicia sativa L.) and their subsequent use as green manure (incorporating fresh plant biomass into soil to enhance nutrient cycling and microbial activity) on fungal diversity and community structure. Three field treatments were organized as follows: (i) unplanted control, (ii) single-oat cultivation, and (iii) oat–vetch intercropping. In the ripening stage of oats development, the plants in the intercropping treatment were ploughed at a depth of 30 cm as green manure. Soil samples at ripening stage and 3 months after ploughing were analyzed. High-throughput sequencing of the ITS2 region, combined with multivariate diversity analyses (alpha and beta diversity, PCA, NMDS, and UniFrac), revealed distinct fungal community profiles across treatments. Ascomycota dominated under conventional and untreated conditions, while Basidiomycota, Mortierellomycota, and Glomeromycota were enriched in intercropped and organically amended plots, notably at intercropping. Intercropping and green manuring significantly increased species richness, evenness, and phylogenetic fungal diversity. These treatments also supported higher abundances of beneficial fungi such as Mortierella, Glomus, and Trichoderma, while reducing potentially pathogenic taxa like Fusarium. Rank–abundance curves and rarefaction analysis confirmed that diversified systems hosted more balanced and complex fungal assemblages. Beta diversity metrics and ordination analyses indicated strong dissimilarities between the conventionally managed and diversified systems. The results showed that intercropping and organic inputs alter fungal community composition and promote microbial resilience and ecological functionality in the rhizosphere. These practices promoted the development of stable and diverse fungal networks essential for sustainable soil management and crop production. Full article
(This article belongs to the Special Issue Soil Health and Plant Microbiome–Bioeffectors Relationship in Sustainable Agriculture, 2nd Edition)
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18 pages, 5210 KB  
Article
Influence Pattern and Mechanism of Increased Nitrogen Deposition and AM Fungi on Soil Microbial Community in Desert Ecosystems
by Hui Wang, Wan Duan, Qianqian Dong, Zhanquan Ji, Wenli Cao, Fangwei Zhang, Wenshuo Li and Yangyang Jia
Microorganisms 2025, 13(12), 2660; https://doi.org/10.3390/microorganisms13122660 - 22 Nov 2025
Viewed by 738
Abstract
With continuous increases in nitrogen (N) deposition in the future, its impacts on terrestrial ecosystems are attracting growing concern. Arbuscular mycorrhiza (AM) fungi play a crucial role in shaping both soil microbial and plant communities. AM fungi play a crucial role in shaping [...] Read more.
With continuous increases in nitrogen (N) deposition in the future, its impacts on terrestrial ecosystems are attracting growing concern. Arbuscular mycorrhiza (AM) fungi play a crucial role in shaping both soil microbial and plant communities. AM fungi play a crucial role in shaping the soil microbial and plant communities, yet their patterns of influence under increased N deposition scenarios remain unclear, particularly in desert ecosystems. Therefore, we conducted a field experiment simulating increased N deposition and AM fungal suppression to assess the effects of increased N deposition and AM fungi on soil microbial communities, employing phospholipid fatty acid (PLFA) biomarker technology in the Gurbantunggut Desert of Xinjiang. We found that increased N deposition promoted soil microbial biomass, including AM fungi, fungi, Actinomycetes (Act), Gram-positive bacteria (G+), Gram-negative bacteria (G−), and Dark Septate Endophyte (DSE). AM fungal suppression significantly increased the content of soil Act and G+. There were clearly and significantly interactive effects of increased N deposition and AM fungi on soil microbial contents. Both increased N deposition and AM fungi caused significant changes in soil microbial community structure. Random forest analysis revealed that soil nitrate N (NO3−-N), Soil Organic Carbon (SOC), and pH were main factors influencing soil microorganisms; soil AM fungi, G+, and Act significantly affected plant Shannon diversity; soil G−, Act, and fungi posed significant effects on plant community biomass. Finally, the structure equation model results indicated that soil fungi, especially AM fungi, were the main soil microorganisms altering the plant community diversity and biomass under increased N deposition. This study reveals the crucial role of AM fungi in regulating soil microbial responses to increased N deposition, providing experimental evidence for understanding how N deposition affects plant communities through soil microorganisms. Full article
(This article belongs to the Special Issue Soil Health and Plant Microbiome–Bioeffectors Relationship in Sustainable Agriculture, 2nd Edition)
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Review

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38 pages, 4443 KB  
Review
The Role of Plant Growth-Promoting Bacteria in Soil Restoration: A Strategy to Promote Agricultural Sustainability
by Mario Maciel-Rodríguez, Francisco David Moreno-Valencia and Miguel Plascencia-Espinosa
Microorganisms 2025, 13(8), 1799; https://doi.org/10.3390/microorganisms13081799 - 1 Aug 2025
Cited by 23 | Viewed by 7907
Abstract
Soil degradation resulting from intensive agricultural practices, the excessive use of agrochemicals, and climate-induced stresses has significantly impaired soil fertility, disrupted microbial diversity, and reduced crop productivity. Plant growth-promoting bacteria (PGPB) represent a sustainable biological approach to restoring degraded soils by modulating plant [...] Read more.
Soil degradation resulting from intensive agricultural practices, the excessive use of agrochemicals, and climate-induced stresses has significantly impaired soil fertility, disrupted microbial diversity, and reduced crop productivity. Plant growth-promoting bacteria (PGPB) represent a sustainable biological approach to restoring degraded soils by modulating plant physiology and soil function through diverse molecular mechanisms. PGPB synthesizes indole-3-acetic acid (IAA) to stimulate root development and nutrient uptake and produce ACC deaminase, which lowers ethylene accumulation under stress, mitigating growth inhibition. They also enhance nutrient availability by releasing phosphate-solubilizing enzymes and siderophores that improve iron acquisition. In parallel, PGPB activates jasmonate and salicylate pathways, priming a systemic resistance to biotic and abiotic stress. Through quorum sensing, biofilm formation, and biosynthetic gene clusters encoding antibiotics, lipopeptides, and VOCs, PGPB strengthen rhizosphere colonization and suppress pathogens. These interactions contribute to microbial community recovery, an improved soil structure, and enhanced nutrient cycling. This review synthesizes current evidence on the molecular and physiological mechanisms by which PGPB enhance soil restoration in degraded agroecosystems, highlighting their role beyond biofertilization as key agents in ecological rehabilitation. It examines advances in nutrient mobilization, stress mitigation, and signaling pathways, based on the literature retrieved from major scientific databases, focusing on studies published in the last decade. Full article
(This article belongs to the Special Issue Soil Health and Plant Microbiome–Bioeffectors Relationship in Sustainable Agriculture, 2nd Edition)
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