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: 30 September 2025 | Viewed by 888

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 (2 papers)

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Research

35 pages, 17263 KiB  
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 (registering DOI) - 7 Jun 2025
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 KiB  
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
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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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