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Microorganisms
Special Issues
Harnessing Beneficial Microbiota in Sustainable Agriculture
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Harnessing Beneficial Microbiota in Sustainable Agriculture

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

Deadline for manuscript submissions: 31 January 2025 | Viewed by 4366

Special Issue Editors

Dr. Mohamed Idbella

E-Mail Website
Guest Editor
Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
Interests: plant–soil microbial interactions; microbial ecology; plant ecology; mycorrhiza
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Giuliano Bonanomi

E-Mail Website
Guest Editor
Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
Interests: plant pathology; soilborne pathogens; botany; ecology; microbiology; soil organic matter dynamics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the face of a rapidly changing climate and the need for sustainable agriculture, harnessing beneficial microbiota has emerged as a promising approach for plant disease management. This strategy leverages the power of naturally occurring microorganisms to protect plants from diseases, reducing the reliance on chemical pesticides. Beneficial microbiota, including bacteria and fungi, inhabit the rhizosphere and phyllosphere of plants, forming intricate relationships that can enhance the plant's resilience against harmful microbes. They function by competing with pathogens for resources, secreting antimicrobial compounds, and activating the plant's own defense mechanisms. As climate change leads to more unpredictable and severe weather patterns, the ability of plants to fend off diseases becomes increasingly important. Recent research has uncovered exciting possibilities for harnessing microbiota, including the development of biopesticides and probiotics for plants. These solutions not only provide effective disease management but also have the potential to improve crop yields and overall agricultural sustainability. However, challenges such as the complexity of microbial communities and their interactions with plants must be addressed. In a changing climate, the smart utilization of beneficial microbiota offers a sustainable and eco-friendly approach to plant disease management, contributing to global food security while reducing the environmental impact of agriculture.

Reviews, original research, and communications are all welcome to contribute to this Special Issue.

Dr. Mohamed Idbella
Prof. Dr. Giuliano Bonanomi
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. 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

  • disease suppression
  • soilborne pathogens
  • beneficial microbiota
  • next-generation sequencing
  • climate change
  • soil health
  • sustainable agriculture

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Published Papers (4 papers)

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Research

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14 pages, 4998 KiB  
Article
Organic Farming Enhances Diversity and Recruits Beneficial Soil Fungal Groups in Traditional Banana Plantations
by Maria Cristina O. Oliveira, Artur Alves, Carla Ragonezi, José G. R. de Freitas and Miguel A. A. Pinheiro De Carvalho
Microorganisms 2024, 12(11), 2372; https://doi.org/10.3390/microorganisms12112372 - 20 Nov 2024
Viewed by 298
Abstract
This study investigates the impact of organic (OF) and conventional farming (CF) on soil fungal communities in banana monoculture plantations on Madeira Island. We hypothesized that OF promotes beneficial fungal groups over harmful ones, sustaining soil health. Soil samples were collected from six [...] Read more.
This study investigates the impact of organic (OF) and conventional farming (CF) on soil fungal communities in banana monoculture plantations on Madeira Island. We hypothesized that OF promotes beneficial fungal groups over harmful ones, sustaining soil health. Soil samples were collected from six plantations (three OF and three CF) for ITS amplicon sequencing to assess fungal diversity. Results showed that OF significantly enhanced fungal alpha-diversity (Shannon–Wiener index) and Evenness. The phylum Ascomycota dominated OF systems, while Basidiomycota prevailed in CF. Mortierella, a beneficial genus, was abundant in OF and is observed in CF but was less evident, being the genus Trechispora the most well represented in CF agrosystems. Additionally, OF was associated with higher soil pH and Mg levels, which correlated positively with beneficial fungal groups. Functional analysis revealed that OF promoted saprotrophic fungi, crucial for the decomposition of organic matter and nutrient cycling. However, both systems exhibited low levels of arbuscular mycorrhizal fungi, likely due to high phosphorus levels. These findings suggest that organic practices can enhance soil fungal diversity and health, although attention to nutrient management is critical to further improving soil–plant–fungi interactions. Full article
(This article belongs to the Special Issue Harnessing Beneficial Microbiota in Sustainable Agriculture)
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17 pages, 1835 KiB  
Article
Bacterial N-Acyl Homoserine Lactone Priming Enhances Leaf-Rust Resistance in Winter Wheat and Some Genomic Regions Are Associated with Priming Efficiency
by Behnaz Soleimani, Heike Lehnert, Adam Schikora, Andreas Stahl, Andrea Matros and Gwendolin Wehner
Microorganisms 2024, 12(10), 1936; https://doi.org/10.3390/microorganisms12101936 - 24 Sep 2024
Viewed by 644
Abstract
Leaf rust (Puccinia triticina) is a common disease that causes significant yield losses in wheat. The most frequently used methods to control leaf rust are the application of fungicides and the cultivation of resistant genotypes. However, high genetic diversity and associated [...] Read more.
Leaf rust (Puccinia triticina) is a common disease that causes significant yield losses in wheat. The most frequently used methods to control leaf rust are the application of fungicides and the cultivation of resistant genotypes. However, high genetic diversity and associated adaptability of pathogen populations hamper achieving durable resistance in wheat. Emerging alternatives, such as microbial priming, may represent an effective measure to stimulate plant defense mechanisms and could serve as a means of controlling a broad range of pathogens. In this study, 175 wheat genotypes were inoculated with two bacterial strains: Ensifer meliloti strain expR+ch (producing N-acyl homoserine lactone (AHL)) or transformed E. meliloti carrying the lactonase gene attM (control). In total, 21 genotypes indicated higher resistance upon bacterial AHL priming. Subsequently, the phenotypic data of 175 genotypes combined with 9917 single-nucleotide polymorphisms (SNPs) in a genome-wide association study to identify quantitative trait loci (QTLs) and associated markers for relative infection under attM and expR+ch conditions and priming efficiency using the Genome Association and Prediction Integrated Tool (GAPIT). In total, 15 QTLs for relative infection under both conditions and priming efficiency were identified on chromosomes 1A, 1B, 2A, 3A, 3B, 3D, 6A, and 6B, which may represent targets for wheat breeding for priming and leaf-rust resistance. Full article
(This article belongs to the Special Issue Harnessing Beneficial Microbiota in Sustainable Agriculture)
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17 pages, 2058 KiB  
Article
Long-Term Application of Biochar Mitigates Negative Plant–Soil Feedback by Shaping Arbuscular Mycorrhizal Fungi and Fungal Pathogens
by Mohamed Idbella, Silvia Baronti, Francesco Primo Vaccari, Ahmed M. Abd-ElGawad and Giuliano Bonanomi
Microorganisms 2024, 12(4), 810; https://doi.org/10.3390/microorganisms12040810 - 17 Apr 2024
Viewed by 1369
Abstract
Negative plant–soil feedback (PSF) arises when localized accumulations of pathogens reduce the growth of conspecifics, whereas positive PSF can occur due to the emergence of mutualists. Biochar, a carbon-rich material produced by the pyrolysis of organic matter, has been shown to modulate soil [...] Read more.
Negative plant–soil feedback (PSF) arises when localized accumulations of pathogens reduce the growth of conspecifics, whereas positive PSF can occur due to the emergence of mutualists. Biochar, a carbon-rich material produced by the pyrolysis of organic matter, has been shown to modulate soil microbial communities by altering their abundance, diversity, and activity. For this reason, to assess the long-term impact of biochar on soil microbiome dynamics and subsequent plant performance, we conducted a PSF greenhouse experiment using field soil conditioned over 10 years with Vitis vinifera (L.), without (e.g., C) or with biochar at two rates (e.g., B and BB). Subsequently, the conditioned soil was employed in a response phase involving either the same plant species or different species, i.e., Medicago sativa (L.), Lolium perenne (L.), and Solanum lycopersicum (L.). We utilized next-generation sequencing to assess the abundance and diversity of fungal pathogens and arbuscular mycorrhizal fungi (AMF) within each conditioned soil. Our findings demonstrate that biochar application exerted a stimulatory effect on the growth of both conspecifics and heterospecifics. In addition, our results show that untreated soils had a higher abundance of grape-specialized fungal pathogens, mainly Ilyonectria liriodendra, with a relative abundance of 20.6% compared to 2.1% and 5.1% in B and BB, respectively. Cryptovalsa ampelina also demonstrated higher prevalence in untreated soils, accounting for 4.3% compared to 0.4% in B and 0.1% in BB. Additionally, Phaeoacremonium iranianum was exclusively present in untreated soils, comprising 12.2% of the pathogens’ population. Conversely, the application of biochar reduced generalist fungal pathogens. For instance, Plenodomus biglobosus decreased from 10.5% in C to 7.1% in B and 2.3% in BB, while Ilyonectria mors-panacis declined from 5.8% in C to 0.5% in B and 0.2% in BB. Furthermore, biochar application was found to enrich the AMF community. Notably, certain species like Funneliformis geosporum exhibited increased relative abundance in biochar-treated soils, reaching 46.8% in B and 70.3% in BB, compared to 40.5% in untreated soils. Concurrently, other AMF species, namely Rhizophagus irregularis, Rhizophagus diaphanus, and Claroideoglomus drummondii, were exclusively observed in soils where biochar was applied. We propose that the alleviation of negative PSF can be attributed to the positive influence of AMF in the absence of strong inhibition by pathogens. In conclusion, our study underscores the potential of biochar application as a strategic agricultural practice for promoting sustainable soil management over the long term. Full article
(This article belongs to the Special Issue Harnessing Beneficial Microbiota in Sustainable Agriculture)
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Review

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18 pages, 809 KiB  
Review
Microbes in Agriculture: Prospects and Constraints to Their Wider Adoption and Utilization in Nutrient-Poor Environments
by Mustapha Mohammed and Felix D. Dakora
Microorganisms 2024, 12(11), 2225; https://doi.org/10.3390/microorganisms12112225 - 2 Nov 2024
Viewed by 753
Abstract
Microbes such as bacteria and fungi play important roles in nutrient cycling in soils, often leading to the bioavailability of metabolically important mineral elements such as nitrogen (N), phosphorus (P), iron (Fe), and zinc (Zn). Examples of microbes with beneficial traits for plant [...] Read more.
Microbes such as bacteria and fungi play important roles in nutrient cycling in soils, often leading to the bioavailability of metabolically important mineral elements such as nitrogen (N), phosphorus (P), iron (Fe), and zinc (Zn). Examples of microbes with beneficial traits for plant growth promotion include mycorrhizal fungi, associative diazotrophs, and the N2-fixing rhizobia belonging to the α, β and γ class of Proteobacteria. Mycorrhizal fungi generally contribute to increasing the surface area of soil-root interface for optimum nutrient uptake by plants. However, when transformed into bacteroids inside root nodules, rhizobia also convert N2 gas in air into ammonia for use by the bacteria and their host plant. Thus, nodulated legumes can meet a high proportion of their N requirements from N2 fixation. The percentage of legume N derived from atmospheric N2 fixation varies with crop species and genotype, with reported values ranging from 50–97%, 24–67%, 66–86% 27–92%, 50–92%, and 40–75% for soybean (Gycine max), groundnut (Arachis hypogea), mung bean (Vigna radiata), pigeon pea (Cajanus cajan), cowpea (Vigna unguiculata), and Kersting’s groundnut (Macrotyloma geocarpum), respectively. This suggests that N2-fixing legumes require little or no N fertilizer for growth and grain yield when grown under field conditions. Even cereals and other species obtain a substantial proportion of their N nutrition from associative and endophytic N2-fixing bacteria. For example, about 12–33% of maize N requirement can be obtained from their association with Pseudomonas, Hebaspirillum, Azospirillum, and Brevundioronas, while cucumber can obtain 12.9–20.9% from its interaction with Paenebacillus beijingensis BJ-18. Exploiting the plant growth-promoting traits of soil microbes for increased crop productivity without any negative impact on the environment is the basis of green agriculture which is done through the use of biofertilizers. Either alone or in combination with other synergistic rhizobacteria, rhizobia and arbuscular mycorrhizal (AM) fungi have been widely used in agriculture, often increasing crop yields but with occasional failures due to the use of poor-quality inoculants, and wrong application techniques. This review explores the literature regarding the plant growth-promoting traits of soil microbes, and also highlights the bottle-necks in tapping this potential for sustainable agriculture. Full article
(This article belongs to the Special Issue Harnessing Beneficial Microbiota in Sustainable Agriculture)
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