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Microorganisms
Special Issues
Microbial Biotechnologies and Microorganism Interactions for Sustainable Agriculture
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Microbial Biotechnologies and Microorganism Interactions for Sustainable Agriculture

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

Deadline for manuscript submissions: 31 October 2025 | Viewed by 3445

Special Issue Editors

Prof. Dr. Dario Rafael Olicón-Hernández

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Guest Editor
Departamento de Micriobiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Casco de Sto Tomás, Alcaldía Miguel Hidalgo, Mexico City C.P. 11340, Mexico
Interests: biotechnology; Industrial microbiology; and biochemistry
Prof. Dr. Guerra-Sanchez Guadalupe

E-Mail Website
Guest Editor
Departamento de Microbiología, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Plan de Carpio y Plan de Ayala S/N Santo Tomás, Miguel Hidalgo, Mexico City C.P. 11340, Mexico
Interests: fungal plant pathogens; plant interaction with filamentous fungi; enzymes in postharvest food preservation; biochemical changes in yeast under nutritional stress; biocontrol; fungal physiology; fungal biotechnology; chitosan action in fungi; physiological changes during Ustilago maydis in-fection; fungal secondary metabolites during plant interaction
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbial biotechnologies have emerged as a cornerstone of sustainable agriculture, offering innovative tools to enhance productivity while preserving environmental integrity. Advances in genetic engineering, fermentation technologies, and bioformulations have paved the way for the development of biofertilizers, biostimulants, and biopesticides. These technologies provide sustainable alternatives to chemical inputs, improving crop yield and resilience.

Equally critical to sustainable agriculture is the intricate network of interactions among microorganisms, which underpin essential ecological processes. Relationships between fungi, bacteria, and other microbes drive nutrient cycling, plant growth promotion, and biocontrol mechanisms. Despite their significance, the dynamics of these interactions and their integration into agricultural systems remain underexplored.

This Special Issue invites high-quality contributions focusing on two key areas: microbial biotechnologies for sustainable agricultural development and the investigation of microorganism interactions with similar objectives. Submissions may include research on biotechnological innovations, bioinoculants, biopesticides, and bioformulations, as well as studies on synergistic and antagonistic microbial interactions that enhance biocontrol and ecosystem health. Contributions addressing the discovery and application of new bioactive molecules, omics-driven insights, and ecological interaction studies are also encouraged. Original research, reviews, and perspectives in these distinct yet complementary fields are welcome to advance the science and practice of sustainable agriculture.

Prof. Dr. Dario Rafael Olicón-Hernández
Prof. Dr. Guerra-Sanchez Guadalupe
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

  • microbial biotechnologies
  • sustainable agriculture
  • biofertilizers
  • biopesticides
  • bioformulations
  • microbial interactions
  • biocontrol mechanisms
  • ecosystem health
  • omics technologies
  • plant growth promotion

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Published Papers (6 papers)

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Research

17 pages, 1409 KiB  
Article
Co-Application of Seaweed Extract (Solieria filiformis) and Silicon: Effect on Sporulation, Mycorrhizal Colonization, and Initial Growth of Mimosa caesalpiniaefolia
by Isaac Alves da Silva, José Lucas Sousa de Andrade, Francisco Luan Almeida Barbosa, Murilo de Sousa Almeida, Marjory Lima Holanda Araújo, Adijailton Jose de Souza, Ademir Sergio Ferreira Araujo, Arthur Prudêncio de Araujo Pereira and Kaio Gráculo Vieira Garcia
Microorganisms 2025, 13(7), 1581; https://doi.org/10.3390/microorganisms13071581 - 4 Jul 2025
Abstract
Seaweed extracts (SEs) and silicon (Si) are known to enhance plant growth under adverse conditions. However, their combined effects on arbuscular mycorrhizal fungi (AMF) are not yet fully understood. This study evaluated the effect of the co-application of an SE and Si on [...] Read more.
Seaweed extracts (SEs) and silicon (Si) are known to enhance plant growth under adverse conditions. However, their combined effects on arbuscular mycorrhizal fungi (AMF) are not yet fully understood. This study evaluated the effect of the co-application of an SE and Si on the AMF spore abundance, mycorrhizal colonization, and early growth of Mimosa caesalpiniaefolia. Plants were grown in a greenhouse for 70 days in soil with or without an SE (Solieria filiformis) and three Si levels (0, 150, and 300 mg kg−1). Growth parameters, AMF spore abundance, mycorrhizal colonization, and plant/soil chemical composition were assessed. SE and Si increased the plant height, stem diameter, number of leaves, and shoot dry mass, while higher Si levels reduced the root dry mass and length. Mycorrhizal colonization was highest (64%) at 150 mg kg−1 Si with SE, whereas AMF spore abundance decreased as Si increased. SE and 300 mg kg−1 Si raised the Si levels in the shoot, while root Si increased only at 300 mg kg−1 Si. Shoot Na increased at 300 mg kg−1 Si without SE, whereas K was highest at 150 mg kg−1 Si with SE. The soil pH, electrical conductivity, and Na increased at 300 mg kg−1 Si, while K and P decreased at this level without SE. These findings indicate that SE and Si co-application benefits early growth and may modulate mycorrhizal symbiosis, highlighting the importance of proper management to maximize plant and soil benefits. Full article
(This article belongs to the Special Issue Microbial Biotechnologies and Microorganism Interactions for Sustainable Agriculture)
19 pages, 2780 KiB  
Article
Volatile Metabolome and Transcriptomic Analysis of Kosakonia cowanii Ch1 During Competitive Interaction with Sclerotium rolfsii Reveals New Biocontrol Insights
by Yoali Fernanda Hernández Gómez, Jacqueline González Espinosa, Griselda Catalina Olvera Rivas, Jackeline Lizzeta Arvizu Gómez, José Humberto Valenzuela Soto, Miguel Angel Ramos López, Aldo Amaro Reyes, Eloy Rodríguez de León, Carlos Saldaña, José Luis Hernández Flores and Juan Campos Guillén
Microorganisms 2025, 13(7), 1483; https://doi.org/10.3390/microorganisms13071483 - 26 Jun 2025
Viewed by 137
Abstract
The volatile organic compounds (VOCs) produced by K. cowanii Ch1 play a significant role in the inhibition of the mycelial growth of phytopathogen strains. As a continuation of our previous studies, we aim to elucidate the mechanisms of the responses of K. cowanii [...] Read more.
The volatile organic compounds (VOCs) produced by K. cowanii Ch1 play a significant role in the inhibition of the mycelial growth of phytopathogen strains. As a continuation of our previous studies, we aim to elucidate the mechanisms of the responses of K. cowanii Ch1 against S. rolfsii during a colonization competence interaction in the presence and absence of a mixture of bacterial VOCs under in vitro conditions. The results of this study showed that, in the absence of bacterial VOCs, K. cowanii Ch1 cannot compete against S. rolfsii, and the RNA-Seq analysis revealed the differential expression of genes related to the oxidative stress response in K. cowanii Ch1 for survival. However, in the presence of bacterial VOCs, an interesting phenotypical response was observed in K. cowanii Ch1, resulting in the mycelial growth inhibition of S. rolfsii. The upregulated genes were related to the siderophore-mediated iron transport system, zinc ion transport system, antibiotic biosynthesis monooxygenase, carbohydrate metabolism, polyketide synthase modules, and related proteins, and katG was probably related to the phenotype resulting in the formation of gas bubbles by K. cowanii. In addition, the VOC profile analyzed at 36 h for bacterial growth revealed a cocktail with an ability to increase the competence of K. cowanii Ch1 against S. rolfsii in vitro and in vivo. This study provides evidence regarding the key role that VOCs play during the colonization competition involving K. cowanii Ch1, the comprehension of which may enable the development of new biocontrol strategies. Full article
(This article belongs to the Special Issue Microbial Biotechnologies and Microorganism Interactions for Sustainable Agriculture)
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18 pages, 1990 KiB  
Article
Evaluation of Microbial Transplantation from High-Productivity Soil to Improve Soybean Performance in Less Productive Farmland
by Danilo Tosta Souza, Aurélio Carneiro Soares Moreira, Hélio Danilo Quevedo and André May
Microorganisms 2025, 13(6), 1177; https://doi.org/10.3390/microorganisms13061177 - 22 May 2025
Viewed by 412
Abstract
Microbial transplantation represents a sustainable strategy to address productivity gaps in agricultural soils by transferring microbiomes that enhance nutrient cycling, pathogen suppression, and stress tolerance. This study evaluates whether probiotic consortia from high-yield soybean soils (donor soil) could improve crop performance in less [...] Read more.
Microbial transplantation represents a sustainable strategy to address productivity gaps in agricultural soils by transferring microbiomes that enhance nutrient cycling, pathogen suppression, and stress tolerance. This study evaluates whether probiotic consortia from high-yield soybean soils (donor soil) could improve crop performance in less productive fields (recipient soil). We developed a host-adapted inoculant from soybean rhizospheres grown in donor soil and applied it to seeds at five concentrations (0.25–10 g/kg seed) in recipient soil, with untreated controls for comparison. To assess crop-specific microbial recruitment, we prepared a parallel bean-derived inoculant under identical conditions. Through 16S rRNA sequencing and growth/yield analysis, we found the following: (1) Distinct bacteriome assemblies between soybean- and bean-derived inoculants, confirming host specificity; (2) Successful enrichment of beneficial taxa (Enterobacteriaceae increased by 15–22%, Rhizobiaceae by 7–12%) despite native community resilience; and (3) Consistent yield improvement trends (4.8–6.2%), demonstrating potential to bridge productivity gaps. These results show that transplanted microbiomes can effectively modulate rhizosphere communities while maintaining ecological balance. This work establishes a scalable approach to address soil productivity limitations through microbiome transplantation. Future research should optimize (a) inoculant composition for specific productivity gaps; (b) delivery systems; and (c) compatibility with resident microbiomes, particularly in systems where niche-specific processes govern microbial establishment. Full article
(This article belongs to the Special Issue Microbial Biotechnologies and Microorganism Interactions for Sustainable Agriculture)
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16 pages, 1694 KiB  
Article
Synergistic Effect of Essential Oils and Rhamnolipid on Xanthomonas citri Subsp. citri
by Maria Olimpia Pereira Sereia, Eduarda Araujo dos Santos, Lucas Prado Leite, Raphael Culim Neves, Vítor Rodrigues Marin, Henrique Ferreira, Jonas Contiero and Daiane Cristina Sass
Microorganisms 2025, 13(5), 1153; https://doi.org/10.3390/microorganisms13051153 - 17 May 2025
Viewed by 496
Abstract
Citrus canker, caused by Xanthomonas citri subsp. citri, is a devastating disease that affects citrus production and trade worldwide. Traditional control methods, based on copper compounds, are effective but pose environmental and health risks due to their toxicity and potential for bioaccumulation. [...] Read more.
Citrus canker, caused by Xanthomonas citri subsp. citri, is a devastating disease that affects citrus production and trade worldwide. Traditional control methods, based on copper compounds, are effective but pose environmental and health risks due to their toxicity and potential for bioaccumulation. This study evaluates the synergistic potential of essential oils (EOs) and rhamnolipids as sustainable alternatives for disease management. Four EOS (citronella, palmarosa, geranium, and clove) were tested for their antibacterial activity. Citronella EO showed a 90% inhibitory concentration (IC 90) of 0.15% (v/v) and a minimum bactericidal concentration of 0.25% (v/v), while the other EOs showed IC 90 and bactericidal activity at 0.06% (v/v). Rhamnolipids (RHLs), biosurfactants produced by Pseudomonas aeruginosa, inhibited X. citri at a concentration of 0.3% (v/v). The combination of citronella EO and RHLs showed a synergistic effect, reducing the inhibitory concentration of citronella by 50% and that of RHLs by more than 90%. In addition, the combined formulation permeabilized more than 80% of bacterial membranes and reduced biofilm formation. In contrast, other oils tested in combination with rhamnolipid showed independent effects. These results indicate that EOs and rhamnolipids represent an environmentally safe strategy for the control of X. citri subsp. citri that overcomes the limitations of conventional methods while reducing environmental and health impacts. Full article
(This article belongs to the Special Issue Microbial Biotechnologies and Microorganism Interactions for Sustainable Agriculture)
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15 pages, 4136 KiB  
Article
Unlocking Nature’s Microbial Defenders: Genetic Mechanisms and Potential Against Monilinia spp. Pathogens
by Augustina Kolytaitė, Ingrida Mažeikienė, Monika Kurgonaitė, Saulė Raklevičiūtė, Gabija Paškevičiūtė and Birutė Frercks
Microorganisms 2025, 13(4), 818; https://doi.org/10.3390/microorganisms13040818 - 3 Apr 2025
Viewed by 443
Abstract
Monilinia spp., which causes brown rot, is one of the most damaging pathogens in stone fruits. Researchers are exploring epiphytic and endophytic microorganisms with the potential to suppress pathogens, control pathogenic microorganisms, and/or promote plant growth. In this study, microorganisms with antagonistic activity [...] Read more.
Monilinia spp., which causes brown rot, is one of the most damaging pathogens in stone fruits. Researchers are exploring epiphytic and endophytic microorganisms with the potential to suppress pathogens, control pathogenic microorganisms, and/or promote plant growth. In this study, microorganisms with antagonistic activity against three Monilinia species were isolated from plum orchard soil and plum fruits. Antagonism tests in vitro showed strong antagonistic properties of six strains of bacteria and two yeast-like fungi against M. fructigena, M. fructicola, and M. laxa, with growth inhibition from 45.5 to 84.6%. The antagonists were identified and characterized at the genetic level using whole genome sequencing (WGS). Genes involved in antibiotic resistance, virulence, secondary metabolite synthesis, and plant growth promotion were identified and characterized through genome mapping, gene prediction, and annotation. None of the microorganisms studied were predicted to be pathogenic to humans. The results of this study indicate that the bacteria Bacillus pumilus, B. velezensis, two strains of Lysinibacillus agricola, Pseudomonas chlororaphis isolated from stone fruit orchard soil, and the yeast-like fungus Aureobasidium pullulans, isolated from plums, are promising candidates for the biological control of Monilinia spp. Full article
(This article belongs to the Special Issue Microbial Biotechnologies and Microorganism Interactions for Sustainable Agriculture)
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18 pages, 2823 KiB  
Article
Fertilization Induced Soil Microbial Shifts Show Minor Effects on Sapindus mukorossi Yield
by Juntao Liu, Zhexiu Yu, Yingyun Gong, Jie Chen, Ling Zhou, Weihua Zhang and Liming Jia
Microorganisms 2025, 13(1), 173; https://doi.org/10.3390/microorganisms13010173 - 15 Jan 2025
Viewed by 802
Abstract
Fertilization can improve soil nutrition and increase the yield of Sapindus mukorossi, but the response of soil microbial communities to fertilization treatments and their correlation with soil nutrition and Sapindus mukorossi yield are unclear. In order to investigate the characteristics of soil [...] Read more.
Fertilization can improve soil nutrition and increase the yield of Sapindus mukorossi, but the response of soil microbial communities to fertilization treatments and their correlation with soil nutrition and Sapindus mukorossi yield are unclear. In order to investigate the characteristics of soil physicochemical qualities and the bacterial community, we carried out a field experiment comparing various quantities of nitrogen (N), phosphorus (P), and potassium (K) fertilizers to the unfertilized control treatments and the yield of Sapindus mukorossi in raw material forests in response to different applications of fertilizers and to try to clarify the interrelation among the three. Results showed that (1) there are significant differences in the effects of different fertilization treatments on the soil properties of Sapindus mukorossi raw material forests. The increase in the application rates of nitrogen or phosphorus fertilizers significantly reduced the soil pH value. (2) Compared with control, the α-diversity of bacterial communities was significantly lower in N3P2K2 and N1P1K2 treatments. Among the dominant groups of soil bacteria at the phylum level, the relative abundance of Chloroflexi showed an increase and then a decrease trend with the increase in N application. The relative abundance of Firmicutes, Bacteroidota, and Fusobacteriota was positively correlated with the application of P and K fertilizers, while the relative abundance of Acidobacteriota and Verrucomicrobiota decreased with the increase in P and K fertilizers. (3) The N2P2K2 treatment produced the highest sapindus yield (1464.58 kg/ha), which increased by 258.67% above the control. (4) Redundancy analysis (RDA) showed that the primary determinants of bacterial community structure were soil pH, total K, and effective P concentration. (5) Structural equation modeling (SEM) showed that soil nutrient content was the main direct factor driving the yield of Sapindus mukorossi, whereas the bacterial community attributes (e.g., diversity and structure) had minor effects on the yield. In summary, the rational use of formulated fertilization can change the bacterial community structure, improve the bacterial diversity, and increase the soil nutrient content, with the latter exerting a significant effect on the improvement of the yield of Sapindus mukorossi. Full article
(This article belongs to the Special Issue Microbial Biotechnologies and Microorganism Interactions for Sustainable Agriculture)
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