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: 31 December 2025 | Viewed by 1186

Special Issue Editors


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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
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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
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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

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Keywords

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

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Published Papers (1 paper)

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Review

38 pages, 4443 KiB  
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
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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
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