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Microorganisms
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Microbial Biocontrol in the Agri-Food Industry, 2nd Edition
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Microbial Biocontrol in the Agri-Food Industry, 2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 4439

Special Issue Editor

Prof. Dr. Maurizio Ciani

E-Mail Website
Guest Editor
Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
Interests: non-conventional yeasts; wine yeast; antimicrobial compounds; fermented beverages; killer yeasts
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, there has been a growing interest in the use of natural antimicrobial compounds to limit or avoid the use of chemical antimicrobials. Natural antimicrobial compounds have potential applications in the food industry and biological control of plant pathogens, as well as therapeutic agents against animal and human infections. Natural antimicrobial compounds can come from plants (essential oils) or from microorganisms (bacteriocins, mycocines, and active peptides). In spite of a wide range of possible applications, however, their exploitation on an industrial level is still limited and needs to be investigated. The actual and possible applications of natural compounds in agri-food are an interesting and growing field. In addition to the use of antimicrobial compounds, the microorganisms themselves can be used in the control of spoilage microorganisms along the entire production chain of agro-industry products. Likewise, the quick development of novelties in this research field needs up-to-date review papers.

In this Special Issue, we invite authors who are leading investigations into this topic to contribute to the knowledge of the use of natural antimicrobial compounds and biocontrol agents in the agri-food industry.

Prof. Dr. Maurizio Ciani
Guest Editor

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

  • antimicrobial compounds
  • food industry
  • control of plant pathogens
  • spoilage microorganisms
  • killer yeasts
  • antimicrobial peptides
  • essential oils

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Related Special Issue

Published Papers (3 papers)

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Research

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38 pages, 4609 KiB  
Article
Genomic Insights into the Bactericidal and Fungicidal Potential of Bacillus mycoides b12.3 Isolated in the Soil of Olkhon Island in Lake Baikal, Russia
by Maria N. Romanenko, Anton E. Shikov, Iuliia A. Savina, Fedor M. Shmatov, Anton A. Nizhnikov and Kirill S. Antonets
Microorganisms 2024, 12(12), 2450; https://doi.org/10.3390/microorganisms12122450 - 28 Nov 2024
Viewed by 1367
Abstract
The dispersal of plant pathogens is a threat to the global economy and food industry which necessitates the need to discover efficient biocontrol agents such as bacteria, fungi, etc., inhibiting them. Here, we describe the Bacillus mycoides strain b12.3 isolated from the soil [...] Read more.
The dispersal of plant pathogens is a threat to the global economy and food industry which necessitates the need to discover efficient biocontrol agents such as bacteria, fungi, etc., inhibiting them. Here, we describe the Bacillus mycoides strain b12.3 isolated from the soil of Olkhon Island in Lake Baikal, Russia. By applying the co-cultivation technique, we found that the strain inhibits the growth of plant pathogens, such as the bacteria Xanthomonas campestris, Clavibacter michiganensis, and Pectobacterium atrospecticum, as well as the fungus Alternaria solani. To elucidate the genomic fundament explaining these activities, we leveraged next-generation whole-genome sequencing and obtained a high-quality assembly based on short reads. The isolate bore seven known BGCs (biosynthetic gene clusters), including those responsible for producing bacillibactin, fengycin, and petrobactin. Moreover, the genome contained insecticidal genes encoding for App4Aa1, Tpp78Ba1, and Spp1Aa1 toxins, thus implicating possible pesticidal potential. We compared the genome with the 50 closest assemblies and found that b12.3 is enriched with BGCs. The genomic analysis also revealed that genomic architecture corresponds to the experimentally observed activity spectrum implying that the combination of produced secondary metabolites delineates the range of inhibited phytopathogens Therefore, this study deepens our knowledge of the biology and ecology of B. mycoides residing in the Lake Baikal region. Full article
(This article belongs to the Special Issue Microbial Biocontrol in the Agri-Food Industry, 2nd Edition)
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20 pages, 3069 KiB  
Article
Systematic Evaluation of Biotic and Abiotic Factors in Antifungal Microorganism Screening
by Gunjan Gupta, Steve Labrie and Marie Filteau
Microorganisms 2024, 12(7), 1396; https://doi.org/10.3390/microorganisms12071396 - 10 Jul 2024
Viewed by 1757
Abstract
Microorganisms have significant potential to control fungal contamination in various foods. However, the identification of strains that exhibit robust antifungal activity poses challenges due to highly context-dependent responses. Therefore, to fully exploit the potential of isolates as antifungal agents, it is crucial to [...] Read more.
Microorganisms have significant potential to control fungal contamination in various foods. However, the identification of strains that exhibit robust antifungal activity poses challenges due to highly context-dependent responses. Therefore, to fully exploit the potential of isolates as antifungal agents, it is crucial to systematically evaluate them in a variety of biotic and abiotic contexts. Here, we present an adaptable and scalable method using a robotic platform to study the properties of 1022 isolates obtained from maple sap. We tested the antifungal activity of isolates alone or in pairs on M17 + lactose (LM17), plate count agar (PCA), and sucrose–allantoin (SALN) culture media against Kluyveromyces lactis, Candida boidinii, and Saccharomyces cerevisiae. Microorganisms exhibited less often antifungal activity on SALN and PCA than LM17, suggesting that the latter is a better screening medium. We also analyzed the results of ecological interactions between pairs. Isolates that showed consistent competitive behaviors were more likely to show antifungal activity than expected by chance. However, co-culture rarely improved antifungal activity. In fact, an interaction-mediated suppression of activity was more prevalent in our dataset. These findings highlight the importance of incorporating both biotic and abiotic factors into systematic screening designs for the bioprospection of microorganisms with environmentally robust antifungal activity. Full article
(This article belongs to the Special Issue Microbial Biocontrol in the Agri-Food Industry, 2nd Edition)
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Review

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46 pages, 1266 KiB  
Review
Endophytic and Rhizospheric Microorganisms: An Alternative for Sustainable, Organic, and Regenerative Bioinput Formulations for Modern Agriculture
by Isabela de L. Valente, João H. C. Wancura, Giovani L. Zabot and Marcio A. Mazutti
Microorganisms 2025, 13(4), 813; https://doi.org/10.3390/microorganisms13040813 - 3 Apr 2025
Viewed by 749
Abstract
Large amounts of chemical fertilizers are still used to suppress pathogens and boost agricultural productivity and food generation. However, their use can cause harmful environmental imbalance. Furthermore, plants typically absorb limited amounts of the nutrients provided by chemical fertilizers. Recent studies are recommending [...] Read more.
Large amounts of chemical fertilizers are still used to suppress pathogens and boost agricultural productivity and food generation. However, their use can cause harmful environmental imbalance. Furthermore, plants typically absorb limited amounts of the nutrients provided by chemical fertilizers. Recent studies are recommending the use of microbiota present in the soil in different formulations, considering that several microorganisms are found in nature in association with plants in a symbiotic, antagonistic, or synergistic way. This ecological alternative is positive because no undesirable significant alterations occur in the environment while stimulating plant nutrition development and protection against damage caused by control pathogens. Therefore, this review presents a comprehensive discussion regarding endophytic and rhizospheric microorganisms and their interaction with plants, including signaling and bio-control processes concerning the plant’s defense against pathogenic spread. A discussion is provided about the importance of these bioinputs as a microbial resource that promotes plant development and their sustainable protection methods aiming to increase resilience in the agricultural system. In modern agriculture, the manipulation of bioinputs through Rhizobium contributes to reducing the effects of greenhouse gases by managing nitrogen runoff and decreasing nitrous oxide. Additionally, mycorrhizal fungi extend their root systems, providing plants with greater access to water and nutrients. Full article
(This article belongs to the Special Issue Microbial Biocontrol in the Agri-Food Industry, 2nd Edition)
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