Advances in Microbial Solutions for Sustainable Agriculture

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Protection and Biotic Interactions".

Deadline for manuscript submissions: 28 February 2026 | Viewed by 5607

Special Issue Editor


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Guest Editor
Research Associate Professor, Chair of Biochemistry and Molecular Biology, University of Belgrade, Faculty of Biology, Studentski trg 16, 11158 Belgrade, Serbia
Interests: plant protection; biological control; biopesticides; Bacillus and Pseudomonas; geomicrobiology; microbiomes

Special Issue Information

Dear Colleagues,

Over the last few decades, the rise in agricultural production has been based mainly on the heavy use of chemical fertilizers and pesticides. The interest in biological control of phytopathogens has particularly increased over the last decade, especially because of the importance of using environmentally friendly alternatives to the extensive use of chemical pesticides for combating pest diseases. Extensive microbiome research in the field of structure and function of the plant microbiome, the pivotal role of plant-associated microbes on plant health and productivity, as well as the “state of the art” new methodologies nowadays, should increase our knowledge and provide a movement from laboratory data to practical applications in sustainable agriculture. Plant-associated microbial communities play key functions in biotic and abiotic stress tolerance as well as nutrient acquisition and carbon and nitrogen cycling. Overall, through numerous mechanisms, beneficial microbes, including antibiosis, toxin production, and nutrient sequestration, directly suppress the proliferation of pathogens and the symptoms of infections in plants. Biological control of plant diseases is not only an alternative to chemical pesticides, but it may also provide control of diseases that cannot be managed by other control strategies. On the other hand, plant growth promotion may come about through direct regulation of phytohormonal activity, increasing root surface area, increasing tolerance to plant diseases, rhizosphere engineering, siderophore production, phosphate solubilization, and the production of active chemical signals. These phenomena have been observed in plant–microbe interactions involving agriculturally important crops such as cereals and legumes. The idea of the now-how development of eco-friendly biopesticides and biofertilizers, and other agricultural biotechnologies, together with molecular studies on the resistance of plants to biotic and abiotic stress and the investigation of interkingdom signaling between plants and plant-associated bacteria, with special attention to emerging phytopathogens, will be the most characteristic activities and outcomes of this Special Issue.

Dr. Ivica Dimkić
Guest Editor

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Keywords

  • plant–pathogen interaction
  • biological control
  • biofertilizers
  • biopesticides
  • interkingdom signaling between plants and plant-associated bacteria

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Published Papers (5 papers)

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Research

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17 pages, 2985 KB  
Article
Corn Stover Biochar Amendment Enhances Nitrogen and Phosphorus Transformations, Microbial Community Diversity, and Enzyme Activities in Agricultural Soil
by Baihui Li, Jie Zhang, Tingting Chang, Qianqian Wu, Hanyu Zheng and Dong Zhang
Plants 2025, 14(17), 2787; https://doi.org/10.3390/plants14172787 - 5 Sep 2025
Viewed by 499
Abstract
Corn stover biochar amendment significantly influences nitrogen (N) and phosphorus (P) transformations, microbial community composition, and enzyme activities in continuous cropping soils. This study aimed to identify the optimal biochar application rate for enhancing N and P nutrient availability in Solanum lycopersicum L. [...] Read more.
Corn stover biochar amendment significantly influences nitrogen (N) and phosphorus (P) transformations, microbial community composition, and enzyme activities in continuous cropping soils. This study aimed to identify the optimal biochar application rate for enhancing N and P nutrient availability in Solanum lycopersicum L. continuous cropping systems, providing theoretical and technical foundations for mitigating continuous cropping obstacles. A soil experiment under rain-out shelters employed four treatments: 1% biochar (BA1), 3% biochar (BA3), 5% biochar (BA5), and a non-amended control (BA0). The results indicated that biochar amendment significantly elevated available phosphorus content in the soil while effectively suppressing its vertical migration; nitrate N content increased under BA1 treatment but decreased in the BA3 and BA5 groups; and the strength of the inhibition effect of biochar treatment on the vertical migration of nitrate N was BA1 > BA5 > BA0 > BA3. The addition of biochar treatment had no significant effect on the content of ammonium N but could inhibit the vertical migration of ammonium N. The addition of biochar treatment could increase the soil’s ammonium N content. The addition of biochar treatment increased soil catalase and urease and sucrase activities, decreased alkaline phosphatase activity, led to the promotion of nitrate reductase activity at low doses and its inhibition at high doses, and resulted in BA1 treatment having the largest soil enzyme index (SEI), which was the most favorable to increase the overall level of soil enzyme activities. Biochar significantly increased the relative abundance of Patescibacteria and Ciliophora while reducing Gemmatimonadota, Acidobacteriota, Nitrospirota, Ascomycota, and Chlorophyta. Comprehensive evaluation using gray relational analysis (GRA) demonstrated that the addition of 5% biochar resulted in the optimal overall performance, enhancing nitrogen and phosphorus transformation, improving microbial community structure, and harmonizing enzyme activities, thereby exhibiting considerable potential for alleviating the nutrient limitations of nitrogen and phosphorus in continuous cropping soils. Full article
(This article belongs to the Special Issue Advances in Microbial Solutions for Sustainable Agriculture)
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26 pages, 1726 KB  
Article
Growth-Promoting Effects of Ten Soil Bacterial Strains on Maize, Tomato, Cucumber, and Pepper Under Greenhouse Conditions
by Jovana Anđelković, Tatjana Mihajilov Krstev, Ivica Dimkić, Nikola Unković, Dalibor Stanković and Nataša Joković
Plants 2025, 14(12), 1874; https://doi.org/10.3390/plants14121874 - 18 Jun 2025
Cited by 1 | Viewed by 1158
Abstract
Beneficial interactions between plants and bacteria are crucial in agricultural practices, as bacteria can improve soil fertility, promote plant growth, and protect plants from pathogens. This study aimed to molecularly identify and characterize soil bacterial isolates and evaluate their effect on the growth [...] Read more.
Beneficial interactions between plants and bacteria are crucial in agricultural practices, as bacteria can improve soil fertility, promote plant growth, and protect plants from pathogens. This study aimed to molecularly identify and characterize soil bacterial isolates and evaluate their effect on the growth of maize (Zea mays L.), tomato (Solanum lycopersici L.), cucumber (Cucumis sativus L.), and pepper (Capsicum annuum L.) under greenhouse conditions. Plant growth parameters, including plant height, root length, and fresh (FW) and dry (DW) weights, were measured. Additionally, pigment extraction and element content analysis using leaves were performed. Among the isolates, the most effective strain in the greenhouse experiment was Bacillus safensis SCF6, which significantly enhanced plant height and fresh weight across all tested plants, with the greatest influence observed in maize plant height (439.42 ± 6.42 mm), fresh weight (14.07 ± 0.87 g plant−1 FW), and dry weight (1.43 ± 0.17 g plant−1 DW) compared to the control (364.67 ± 10.33 mm, 9.20 ± 1.16 g plant−1 FW, and 0.92 ± 0.15 g plant−1 DW, respectively). Other strains also demonstrated notable results, with Microbacterium testaceum SCF4, Bacillus mojavensis SCF8, and Pseudomonas putida SCF9 showing the highest plant growth-promoting effects on pepper, tomato, and cucumber, respectively. Pseudomonas putida SCF9 demonstrated strong antifungal activity against Monilinia laxa, with a percentage of mycelial growth inhibition (PGI) of 72.62 ± 2.06%, while Bacillus subtilis SCF1 exhibited effects against Botrytis cinerea (PGI = 69.57 ± 4.35%) and Cercospora sp. (PGI = 63.11 ± 1.12%). The development and application of beneficial bacterial inoculants or their formulated products can contribute to environmentally friendly farming practices and global food security. Full article
(This article belongs to the Special Issue Advances in Microbial Solutions for Sustainable Agriculture)
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35 pages, 17263 KB  
Article
The Influence of Bacterial Inoculants and a Biofertilizer on Maize Cultivation and the Associated Shift in Bacteriobiota During the Growing Season
by Katarina Kruščić, Aleksandra Jelušić, Matjaž Hladnik, Tamara Janakiev, Jovana Anđelković, Dunja Bandelj and Ivica Dimkić
Plants 2025, 14(12), 1753; https://doi.org/10.3390/plants14121753 - 7 Jun 2025
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Abstract
Maize (Zea mays L.) relies heavily on nitrogen and phosphorus inputs, typically supplied through organic and inorganic fertilizers. However, excessive agrochemical use threatens soil fertility and environmental health. Sustainable alternatives, such as poultry manure (PM) and plant growth-promoting rhizobacteria (PGPR), offer promising [...] Read more.
Maize (Zea mays L.) relies heavily on nitrogen and phosphorus inputs, typically supplied through organic and inorganic fertilizers. However, excessive agrochemical use threatens soil fertility and environmental health. Sustainable alternatives, such as poultry manure (PM) and plant growth-promoting rhizobacteria (PGPR), offer promising solutions. This study examines the effects of a phytobiotic bacterial formulation (PHY), composed of Bacillus subtilis and Microbacterium sp., applied alone and in combination with PM, on maize’s rhizosphere bacteriobiome across key growth stages. Field trials included four treatments: a control, PHY-coated seeds, PM, and combined PHY_PM. The results show that early in development, the PM-treated rhizospheres increased the abundance of beneficial genera such as Sphingomonas, Microvirga, and Streptomyces, though levels declined in later stages. The PHY_PM-treated roots in the seedling phase showed a reduced abundance of taxa like Chryseobacterium, Pedobacter, Phyllobacterium, Sphingobacterium, and Stenotrophomonas, but this effect did not persist. In the PM-treated roots, Flavisolibacter was significantly enriched at harvesting. Overall, beneficial bacteria improved microbial evenness, and the PHY_PM treatment promoted bacterial diversity and maize growth. A genome analysis of the PHY strains revealed plant-beneficial traits, including nutrient mobilization, stress resilience, and biocontrol potential. This study highlights the complementarity of PM and PGPR, showing how their integration reshapes bacteriobiome and correlates with plant parameters in sustainable agriculture. Full article
(This article belongs to the Special Issue Advances in Microbial Solutions for Sustainable Agriculture)
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19 pages, 5695 KB  
Article
Diversified Soil Types Differentially Regulated the Peanut (Arachis hydropoaea L.) Growth and Rhizosphere Bacterial Community Structure
by Wenfei Lan, Hong Ding, Zhimeng Zhang, Fan Li, Hao Feng, Qing Guo, Feifei Qin, Guanchu Zhang, Manlin Xu and Yang Xu
Plants 2025, 14(8), 1169; https://doi.org/10.3390/plants14081169 - 9 Apr 2025
Cited by 1 | Viewed by 791
Abstract
Peanut (Arachis hydropoaea L.) demonstrates a prominent adaptability to diverse soil types. However, the specific effects of soil types on peanut growth and bacterial communities remain elusive. This study conducted a thorough examination of the agronomic traits, the corresponding physicochemical properties, and [...] Read more.
Peanut (Arachis hydropoaea L.) demonstrates a prominent adaptability to diverse soil types. However, the specific effects of soil types on peanut growth and bacterial communities remain elusive. This study conducted a thorough examination of the agronomic traits, the corresponding physicochemical properties, and bacterial structure of rhizosphere soil in acidic (AT), neutral (NT), and saline–alkali (ST) soils, elucidating the internal relationship between soil type and peanut yield. Our results showed that different soil types exhibited significant differences in peanut yield, with ST demonstrating the lowest yield per plant, showing an 85.05% reduction compared to NT. Furthermore, available phosphorus content, urease, and invertase activities were substantially reduced in both ST and AT, particularly in ST by 95.35%, 38.57%, and 62.54%, respectively. Meanwhile, metagenomic sequencing unveiled a notable decline in Bradyrhizobium and Streptomyces in these soils, which is crucial for soil improvement. Further metabolic pathway analysis revealed that the reduction in pathways related to soil remediation, fertility improvement, and stress response in AT and ST may lead to slower peanut growth. In conclusion, peanuts cultivated in acidic and saline–alkali soils can increase yield via implementing soil management practices such as improving soil quality and refining micro-environments. Our study provides practical applications for enhancing peanut yield in low- to medium-yield fields. Full article
(This article belongs to the Special Issue Advances in Microbial Solutions for Sustainable Agriculture)
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Review

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15 pages, 1118 KB  
Review
Bacterial Cyclic Lipopeptides as Triggers of Plant Immunity and Systemic Resistance Against Pathogens
by Ning Ding, Hansong Dong and Marc Ongena
Plants 2025, 14(17), 2644; https://doi.org/10.3390/plants14172644 - 25 Aug 2025
Viewed by 988
Abstract
Cyclic lipopeptides (CLPs) are secondary metabolites produced by plant-beneficial bacteria, including Bacillus, Pseudomonas, Paenibacillus, Burkholderia, Serratia, and Streptomyces species. Of these bacterial sources, CLPs from Bacillus and Pseudomonas have been studied most extensively for their role in plant [...] Read more.
Cyclic lipopeptides (CLPs) are secondary metabolites produced by plant-beneficial bacteria, including Bacillus, Pseudomonas, Paenibacillus, Burkholderia, Serratia, and Streptomyces species. Of these bacterial sources, CLPs from Bacillus and Pseudomonas have been studied most extensively for their role in plant immunity, particularly in mediating induced systemic resistance. With this review, we provide a unique and comprehensive survey of CLPs from plant-beneficial bacteria described for this function. We consolidate existing knowledge on their role in triggering induced systemic resistance across various plant–pathogen systems and elucidate the underlying mechanisms of symptom suppression. We also discuss the need for further mechanistic studies, but also for implementing each step of the process, leading to marketable CLP-based products used as alternatives to chemicals in sustainable agriculture. Full article
(This article belongs to the Special Issue Advances in Microbial Solutions for Sustainable Agriculture)
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