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Microorganisms
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Soil Health and Plant-Microbiome-Bioeffectors Relationship in Sustainable Agriculture
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Soil Health and Plant-Microbiome-Bioeffectors Relationship in Sustainable Agriculture

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 31 March 2025 | Viewed by 12463

Special Issue Editors

Prof. Dr. Nikolay Vassilev

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Guest Editor
Department of Chemical Engineering, 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
Dr. Stefan Shilev

E-Mail Website
Guest Editor
Associate Professor, 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 habitat’s characteristics. The progress achieved in the last years in agricultural practices and circular bioeconomy, 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, hence 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, not restrictive, 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 Bojkov Vassilev
Dr. Stefan Shilev
Guest Editors

Manuscript Submission Information

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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 (7 papers)

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18 pages, 2428 KiB  
Article
Fertilization Type Differentially Affects Barley Grain Yield and Nutrient Content, Soil and Microbial Properties
by Stefan Shilev, Anyo Mitkov, Vanya Popova, Ivelina Neykova, Nikolay Minev, Wieslaw Szulc, Yordan Yordanov and Mariyan Yanev
Microorganisms 2024, 12(7), 1447; https://doi.org/10.3390/microorganisms12071447 - 17 Jul 2024
Viewed by 822
Abstract
The use of artificial fertilizers follows the intensification of agricultural production as a consequence of population growth, which leads to soil depletion, loss of organic matter, and pollution of the environment and production. This can be overcome by increasing the use of organic [...] Read more.
The use of artificial fertilizers follows the intensification of agricultural production as a consequence of population growth, which leads to soil depletion, loss of organic matter, and pollution of the environment and production. This can be overcome by increasing the use of organic fertilizers in agriculture. In the present study, we investigated the effect of using vermicompost, biochar, mineral fertilizer, a combination of vermicompost and mineral fertilizer, and an untreated control on alluvial-meadow soil on the development of fodder winter barley Hordeum vulgare L., Zemela cultivar. We used a randomized complete block design of four replications per treatment. Barley grain yield, number of plants, and soil and microbiological parameters were studied. We found statistically proven highest grain yield and grain protein values when applying vermicompost alone, followed by the combined treatment and mineral fertilizer. The total organic carbon was increased by 70.2% in the case of vermicompost and by 44% in the case of combined treatment, both compared to the control. Thus, soil microbiome activity and enzyme activities were higher in vermicompost treatment, where the activity of β-glucosidase was 29.4% higher in respect to the control, 37.5% to the mineral fertilizer, and 24.5% to the combined treatments. In conclusion, our study found the best overall performance of vermicompost compared to the rest of the soil amendments. Full article
(This article belongs to the Special Issue Soil Health and Plant-Microbiome-Bioeffectors Relationship in Sustainable Agriculture)
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33 pages, 30030 KiB  
Article
Exploring the Impact of Coconut Peat and Vermiculite on the Rhizosphere Microbiome of Pre-Basic Seed Potatoes under Soilless Cultivation Conditions
by Kan Yan, Yanni Ma, Songming Bao, Wandi Li, Yunjiao Wang, Chao Sun, Xin Lu and Juan Ran
Microorganisms 2024, 12(3), 584; https://doi.org/10.3390/microorganisms12030584 - 14 Mar 2024
Cited by 2 | Viewed by 1975
Abstract
Soilless cultivation of potatoes often utilizes organic coconut peat and inorganic vermiculite as growing substrates. The unique microbial communities and physicochemical characteristics inherent to each substrate significantly influence the microecological environment crucial for potato growth and breeding. This study analyzed environmental factors within [...] Read more.
Soilless cultivation of potatoes often utilizes organic coconut peat and inorganic vermiculite as growing substrates. The unique microbial communities and physicochemical characteristics inherent to each substrate significantly influence the microecological environment crucial for potato growth and breeding. This study analyzed environmental factors within each substrate and employed Illumina sequencing alongside bioinformatics tools to examine microbial community structures, their correlation with environmental factors, core microbial functions, and the dynamics of microbial networks across various samples. These included pure coconut peat (CP1) and pure vermiculite (V1), substrates mixed with organic fertilizer for three days (CP2 and V2), and three combinations cultivated with potatoes for 50 days (CP3, V3, and CV3—a 1:1 mix of coconut peat and vermiculite with organic fertilizer). Vermiculite naturally hosts a more diverse microbial community. After mixing with fertilizer and composting for 3 days, and 50 days of potato cultivation, fungal diversity decreased in both substrates. Coconut peat maintains higher bacterial diversity and richness compared to vermiculite, harboring more beneficial bacteria and fungi, resulting in a more complex microbial network. However, vermiculite shows lower bacterial diversity and richness, with an accumulation of pathogenic microorganisms. Among the 11 environmental factors tested, water-soluble nitrogen (WSN), total nitrogen (TN), available potassium (AK), total organic carbon (TOC) and air-filled porosity (AFP) were significantly associated with microbial succession in the substrate.The nutritional type composition and interaction patterns of indigenous microorganisms differ between vermiculite and coconut peat. Adding abundant nutrients significantly affects the stability and interaction of the entire microbial community, even post-potato cultivation. When using vermiculite for soilless cultivation, precise control and adjustment of nutrient addition quantity and frequency are essential. Full article
(This article belongs to the Special Issue Soil Health and Plant-Microbiome-Bioeffectors Relationship in Sustainable Agriculture)
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12 pages, 3928 KiB  
Article
Variation of Soil Bacterial Communities in Forest Soil Contaminated with Chainsaw Lubricants
by Ikhyun Kim, Manh Ha Nguyen, Sanggon Lee, Byoungkoo Choi and Keumchul Shin
Microorganisms 2024, 12(3), 508; https://doi.org/10.3390/microorganisms12030508 - 1 Mar 2024
Viewed by 1296
Abstract
Pollutants can exist in the soil for a long time and alter the bacterial community. Using lubricants to prevent the wear of chainsaw blades is necessary for thinning activities and wood harvesting. We investigated the influences of soil contamination with chainsaw lubricants on [...] Read more.
Pollutants can exist in the soil for a long time and alter the bacterial community. Using lubricants to prevent the wear of chainsaw blades is necessary for thinning activities and wood harvesting. We investigated the influences of soil contamination with chainsaw lubricants on soil bacterial communities. Bio-oil, mineral oil, and recycled oil were scattered on each treatment to investigate variations in soil bacterial structure during treated periods using the Illumina MiSeq sequencing platform. The results obtained were 5943 ASVs, 5112 ASVs, and 6136 ASVs after treatment at one month, six months, and twelve months, respectively. There was a significant difference in Shannon and Simpson indices between treatments and controls. A total of 46 bacterial genera with an average relative abundance of more than 1.0% were detected in all soil samples. Massilia was the most common genus detected in control at one month, with an average relative abundance of 14.99%, while Chthoniobacter was the most abundant genus detected in bio-oil, mineral oil, and recycled oil treatments at one month, with an average relative abundance of 13.39%, 14.32%, and 10.47%, respectively. Among the three chainsaw lubricants, bio-oil and mineral oil had fewer impacts than recycled oil. The abundances of several functional bacteria groups in the bio-oil treatment were higher than in other treatments and controls. Our results indicated that different chainsaw lubricants and their time of application affected the soil bacterial community composition. Full article
(This article belongs to the Special Issue Soil Health and Plant-Microbiome-Bioeffectors Relationship in Sustainable Agriculture)
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11 pages, 1553 KiB  
Article
Soil Fertilization with Palm Oil Mill Effluent Has a Short-Term Effect on the Bacterial Diversity of an Amazonian Agricultural Land Area
by Johnes Pinto Sanches, Sávio Souza Costa, Diego Assis das Graças, Artur Silva, Guilherme Costa Baião, Rennan G. Moreira, Marcelo Murad Magalhães, Roberto Lisboa Cunha and Rafael Azevedo Baraúna
Microorganisms 2024, 12(3), 507; https://doi.org/10.3390/microorganisms12030507 - 1 Mar 2024
Viewed by 1578
Abstract
Palm oil derived from the fruits of Elaeis guineensis Jacq. has global economic importance and is largely produced in tropical regions. The palm oil production process leads to a highly polluting waste called palm oil mill effluent (POME). A strategy commonly used by [...] Read more.
Palm oil derived from the fruits of Elaeis guineensis Jacq. has global economic importance and is largely produced in tropical regions. The palm oil production process leads to a highly polluting waste called palm oil mill effluent (POME). A strategy commonly used by producers to overcome environmental issues and to improve soil fertility is the reuse of POME as a fertilizer due to the chemical and biological characteristics of the effluent. In this research, three groups were analyzed: soil without POME application (control group) and soil samples after 4 and 9 days of POME application. An environmental DNA metabarcoding approach was used. eDNA was extracted, and the V4 region of the 16S rRNA gene was amplified and sequenced in the Illumina MiSeq platform. The abundance of Proteobacteria (48.1%) and Firmicutes (9.0%) was higher in fertilized soil, while Bacteroidetes (20.3%) and Verrucomicrobia (7.8%) were more abundant in control soil. Additionally, the effluent seemed to modify soil characteristics favoring taxa responsible for the mineralization of organic compounds and nitrogen fixation such as species of Gammaproteobacteria class. Our study highlights the influence of POME on soil biological components and contributes to the sustainable production of palm oil in the Amazon. Full article
(This article belongs to the Special Issue Soil Health and Plant-Microbiome-Bioeffectors Relationship in Sustainable Agriculture)
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13 pages, 2615 KiB  
Article
The Win–Win Effects of an Invasive Plant Biochar on a Soil–Crop System: Controlling a Bacterial Soilborne Disease and Stabilizing the Soil Microbial Community Network
by Sheng Wang, Lei Wang, Sicong Li, Tiantian Zhang and Kunzheng Cai
Microorganisms 2024, 12(3), 447; https://doi.org/10.3390/microorganisms12030447 - 22 Feb 2024
Cited by 2 | Viewed by 1379
Abstract
Biochar is increasingly being recognized as an effective soil amendment to enhance plant health and improve soil quality, but the complex relationships among biochar, plant resistance, and the soil microbial community are not clear. In this study, biochar derived from an invasive plant [...] Read more.
Biochar is increasingly being recognized as an effective soil amendment to enhance plant health and improve soil quality, but the complex relationships among biochar, plant resistance, and the soil microbial community are not clear. In this study, biochar derived from an invasive plant (Solidago canadensis L.) was used to investigate its impacts on bacterial wilt control, soil quality, and microbial regulation. The results reveal that the invasive plant biochar application significantly reduced the abundance of Ralstonia solanacearum in the soil (16.8–32.9%) and wilt disease index (14.0–49.2%) and promoted tomato growth. The biochar treatment increased the soil organic carbon, nutrient availability, soil chitinase, and sucrase activities under pathogen inoculation. The biochar did not influence the soil bacterial community diversity, but significantly increased the relative abundance of beneficial organisms, such as Bacillus and Sphingomonas. Biochar application increased the number of nodes, edges, and the average degree of soil microbial symbiotic network, thereby enhancing the stability and complexity of the bacterial community. These findings suggest that the invasive plant biochar produces win–win effects on plant–soil systems by suppressing soilborne wilt disease, enhancing the stability of the soil microbial community network, and promoting resource utilization, indicating its good potential in sustainable soil management. Full article
(This article belongs to the Special Issue Soil Health and Plant-Microbiome-Bioeffectors Relationship in Sustainable Agriculture)
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22 pages, 6878 KiB  
Article
Multi-Generation Ecosystem Selection of Rhizosphere Microbial Communities Associated with Plant Genotype and Biomass in Arabidopsis thaliana
by Nachiket Shankar, Prateek Shetty, Tatiana C. Melo and Rick Kesseli
Microorganisms 2023, 11(12), 2932; https://doi.org/10.3390/microorganisms11122932 - 6 Dec 2023
Cited by 1 | Viewed by 1441
Abstract
The role of the microbiome in shaping the host’s phenotype has emerged as a critical area of investigation, with implications in ecology, evolution, and host health. The complex and dynamic interactions involving plants and their diverse rhizospheres’ microbial communities are influenced by a [...] Read more.
The role of the microbiome in shaping the host’s phenotype has emerged as a critical area of investigation, with implications in ecology, evolution, and host health. The complex and dynamic interactions involving plants and their diverse rhizospheres’ microbial communities are influenced by a multitude of factors, including but not limited to soil type, environment, and plant genotype. Understanding the impact of these factors on microbial community assembly is key to yielding host-specific and robust benefits for plants, yet it remains challenging. Here, we conducted an artificial ecosystem selection experiment for eight generations of Arabidopsis thaliana Ler and Cvi to select soil microbiomes associated with a higher or lower biomass of the host. This resulted in divergent microbial communities shaped by a complex interplay between random environmental variations, plant genotypes, and biomass selection pressures. In the initial phases of the experiment, the genotype and the biomass selection treatment had modest but significant impacts. Over time, the plant genotype and biomass treatments gained more influence, explaining ~40% of the variation in the microbial community’s composition. Furthermore, a genotype-specific association of plant-growth-promoting rhizobacterial taxa, Labraceae with Ler and Rhizobiaceae with Cvi, was observed under selection for high biomass. Full article
(This article belongs to the Special Issue Soil Health and Plant-Microbiome-Bioeffectors Relationship in Sustainable Agriculture)
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11 pages, 466 KiB  
Article
The Combined Applications of Microbial Inoculants and Organic Fertilizer Improve Plant Growth under Unfavorable Soil Conditions
by Malek Al Methyeb, Silke Ruppel, Bettina Eichler-Löbermann and Nikolay Vassilev
Microorganisms 2023, 11(7), 1721; https://doi.org/10.3390/microorganisms11071721 - 30 Jun 2023
Cited by 2 | Viewed by 2500
Abstract
The performance of two bio-inoculants either in single or in combined applications with organic fertilizer was tested to determine their effect on plant growth and yield under normal and unfavorable field conditions such as low pH value and low content of P. Arbuscular [...] Read more.
The performance of two bio-inoculants either in single or in combined applications with organic fertilizer was tested to determine their effect on plant growth and yield under normal and unfavorable field conditions such as low pH value and low content of P. Arbuscular Mycorrhiza Fungi (AMF; three species of Glomus) and the plant-growth-promoting bacterial strain Kosakonia radicincitans DSM16656 were applied to barley in a two-year field experiment with different soil pH levels and available nutrients. Grain yield; contents of P, N, K, and Mg; and soil microbial parameters were measured. Grain yield and the content of nutrients were significantly increased by the applications of mineral fertilizer, organic fertilizer, AMF, and K. radicincitans, and the combined application of organic fertilizer with AMF and with K. radicincitans over the control under normal growth conditions. Under low-pH and low-P conditions, only the combined application of the organic fertilizer with K. radicincitans and organic fertilizer with AMF could increase the grain yield and content of nutrients of barley over the control. Full article
(This article belongs to the Special Issue Soil Health and Plant-Microbiome-Bioeffectors Relationship in Sustainable Agriculture)
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