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Advanced Research on Biological Control of Plant Disease or Microbial Interactions (2nd Edition)

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: closed (15 December 2024) | Viewed by 18236

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Dr. Tomislav Cernava

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Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz 8010, Austria
Interests: plant microbiota; plant–microbe interactions; metagenomics; biological control; microbial VOCs
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Dr. Beibei Ge

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Institute of Plant Protection (IPP), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
Interests: mechanism of biosynthesis regulation of streptomyces; development and utilization of agricultural microorganisms
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant diseases are caused by a large number of plant pathogens, with fungi, bacteria, and virus being the main cause of the loss of crop yield and quality worldwide. Although several control strategies were developed to reduce the negative effects of plant diseases, biological control remains an environmentally friendly and cost-effective green technique in environmental protection and agricultural production; it generally uses selected bioresources, including beneficial microorganisms. This Special Issue will offer comprehensive coverage of the general principles and advances in the “Biological Control of Plant Disease or Microbial interactions”. I welcome and invite authors to submit a review article, original research article, or short communication on topics related to the modes of action and applications of biocontrol agents in the control of plant diseases, interactions between plant pathogens and biocontrol agents, and an understanding of biological control agents and their mechanisms.

Reviews, original research articles, and communications are all welcome.

The Special Issue entitled "Advanced Research on Biological Control of Plant Disease or Microbial interactions 2.0" is the extension volume of its original Special Issue (https://www.mdpi.com/journal/microorganisms/special_issues/biological_control_disease_interactions), aims to present the latest research findings on any aspect of biological control. Some of the main topics include, but are not limited to, the following:

Interactions between plant pathogens and biocontrol agents;
The functional study of pathogenesis-related genes or effectors;
Microbial volatile organic compounds (mVOCs);
PGPR or PGPF related to ISR and plant growth promotion;
Modes of action and applications of biocontrol agents to control plant diseases;
The role of secondary metabolites and biocontrol agents in plant–pathogen interactions;
Advances in the understanding of biological control agents and their mechanisms;
Metagenomics approaches in systems microbiology.

Dr. Tomislav Cernava
Dr. Beibei Ge
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.

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Published Papers (11 papers)

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17 pages, 5242 KiB

Open AccessArticle

Investigating the Rhizosphere Fungal Communities of Healthy and Root-Rot-Infected Lycium barbarum in the Tsaidam Basin, China

by Guozhen Duan, Guanghui Fan, Jianling Li, Min Liu and Youchao Qi

Microorganisms 2024, 12(12), 2447; https://doi.org/10.3390/microorganisms12122447 - 28 Nov 2024

Viewed by 730

Abstract

Lycium barbarum is a plant of considerable economic importance in China. However, root rot poses a significant threat to its yield and quality, leading to substantial economic losses. The disparities in rhizosphere soil fungal communities between healthy and root-rot-affected L. barbarum have not been thoroughly explored. Delving into the dynamics between these fungal communities and the onset of root rot may provide pivotal insights for the biological control of this disease in L. barbarum, as well as aid in identifying fungi associated with the condition. In this study, we utilized rhizosphere soil samples from Ningqi No. 1, a distinguished cultivar of L. barbarum, as our experimental material. We assessed the composition and diversity of fungal communities in both diseased (D) and healthy (H) samples using Illumina MiSeq sequencing technology. The study’s findings revealed that the mean concentrations of total nitrogen (TN) and soil organic matter (SOM) were significantly higher in the healthy specimens when contrasted with the diseased ones, while the pH levels were notably increased in the latter group. Additionally, the alpha-diversity of fungal communities was observed to be greater within the healthy samples as opposed to the diseased samples. Marked distinctions in fungal diversity were discerned between the healthy (H) and diseased (D) samples. Ascomycota was identified as the predominant fungal phylum in both groups. In the healthy samples, beneficial fungi such as Plectosphaerella and Mortierella were prevalent, in contrast to the diseased samples, the relative abundances of Embellisia and Alternaria demonstrated remarkable increases of 89.59% and 87.41%, respectively. Non-metric Multidimensional Scaling (NMDS) illustrated clear distinctions in the composition of fungal communities between the healthy and diseased samples. Redundancy Analysis (RDA) indicated total nitrogen (TN), organic matter (SOM), total phosphorus (TP), Available Potassium (AK), pH, and Total Potassium (TK). Notably, pH showed a stronger correlation with the diseased samples, while TN and SOM were more significantly associated with the healthy samples. Full article

(This article belongs to the Special Issue Advanced Research on Biological Control of Plant Disease or Microbial Interactions (2nd Edition))

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21 pages, 8261 KiB

Open AccessArticle

Optimization of Fermentation and Biocontrol Efficacy of Bacillus atrophaeus XHG-1-3m2

by Ziyan Xu, Hailong Lu, Wanbin Shi, Xinmei Zhou, Jianxin Ren, Yanling Zhang and Rong Ma

Microorganisms 2024, 12(11), 2134; https://doi.org/10.3390/microorganisms12112134 - 24 Oct 2024

Cited by 3 | Viewed by 1274

Abstract

Biological control plays an increasingly important role in various aspects of modern agriculture and forestry. Identifying biocontrol strains with commercial potential for effective disease management is currently a focal point in biological control research. In this study, Bacillus atrophaeus XHG-1-3m2, a strain with significant biocontrol potential against Wilsonomyces carpophilus causing shot hole disease in wild apricots, was developed. The study determined the antibacterial activity of the fermentation broth, the optimal fermentation medium composition and conditions, and explored its effectiveness in controlling Wilsonomyces carpophilus. The optimal fermentation medium for strain XHG-1-3m2 comprises 12.5 g/L yeast extract, 12.5 g/L soy peptone, 10.0 g/L sodium chloride, 1 g/L ammonium chloride, 1 g/L potassium dihydrogen phosphate, 1 g/L disodium hydrogen phosphate, and 0.5 g/L magnesium sulfate heptahydrate. With an initial pH of 7.0, a liquid volume of 40%, an inoculum volume of 3%, and shaking incubation at 28 °C for 24 h, the viable cell count reached 14 × 10⁹ CFU/mL. In vitro and in vivo tests on leaves revealed that the fermentation broth and the biocontrol biofertilizer derived from this strain inhibited the leaf lesions caused by Wilsonomyces carpophilus on wild apricots, achieving inhibition rates of 94.62% and 82.46%, respectively. Full article

(This article belongs to the Special Issue Advanced Research on Biological Control of Plant Disease or Microbial Interactions (2nd Edition))

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20 pages, 10480 KiB

Open AccessArticle

Hass Avocado (Persea americana Mill) Peel Extract Reveals Antimicrobial and Antioxidant Properties against Verticillium theobromae, Colletotrichum musae, and Aspergillus niger Pathogens Affecting Musa acuminata Colla Species, in Ecuador

by Caterine Donoso, Mihai A. Raluca, Stephanie Chávez-Jinez and Edwin Vera

Microorganisms 2024, 12(9), 1929; https://doi.org/10.3390/microorganisms12091929 - 23 Sep 2024

Cited by 1 | Viewed by 1832

Abstract

The utilization of agroindustrial residues, such as avocado peel, as a source of bioactive compounds with antioxidant properties has garnered significant attention. In this study, we investigated the antioxidant potential using the DPPH (2,2-diphenyl-1-picrylhydrazyl) and ORAC (oxygen radical absorbance capacity) methods, along with the antimicrobial activity of phenolic compounds extracted from Hass avocado peel. These soluble polyphenols were quantified and identified using high-performance liquid chromatography (HPLC). The research focused on their effects against three fungal pathogens, Verticillium theobromae, Colletotrichum musae, and Aspergillus niger, which significantly impact banana crops, an essential agricultural commodity in Ecuador. The results have revealed that the application of 80% ethanol as an organic solvent led to increased soluble polyphenol content compared to 96% ethanol. Extraction time significantly influenced the phenolic content, with the highest values obtained at 90 min. Interestingly, despite substantial mycelial growth observed across all extract concentrations, the antifungal effect varied among the pathogens. Specifically, V. theobromae exhibited the highest sensitivity, while C. musae and A. niger were less affected. These results underscore the importance of considering both antioxidant and antimicrobial properties when evaluating natural extracts for potential applications in plant disease management. Full article

(This article belongs to the Special Issue Advanced Research on Biological Control of Plant Disease or Microbial Interactions (2nd Edition))

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15 pages, 5552 KiB

Open AccessArticle

Evaluation of the Antifungal and Biochemical Activities of Fungicides and Biological Agents against Ginseng Sclerotinia Root Rot Caused by Sclerotinia nivalis

by Shi Feng, Chunlin Wang, Zhaoyang Xu, Baozhu Dou, Xue Wang, Lina Yang, Baohui Lu and Jie Gao

Microorganisms 2024, 12(9), 1761; https://doi.org/10.3390/microorganisms12091761 - 25 Aug 2024

Viewed by 1137

Abstract

The objective of this study was to identify effective agents for the prevention and control of ginseng Sclerotinia root rot disease caused by Sclerotinia nivalis. The inhibitory effects of 16 chemical fungicides and 10 biocontrol agents (strains) on mycelial growth and sclerotium formation in S. nivalis were determined using a plate confrontation essay. The results showed that the best chemical agents for inhibiting the mycelial growth and sclerotium formation of S. nivalis were fluconazole and fludioxonil, while Bacillus amyloliquefaciens FS6 and B. subtilis (Kono) were the best biocontrol agents (strains). The results of field trials in 2022 and 2023 showed that the control effects of fluconazole and fludioxonil on ginseng Sclerotinia root rot disease were 90.60–98.16%, and those of the biocontrol agents B. amyloliquefaciens FS6 and B. subtilis (Kono) were 94.80–97.24%, respectively. Chemical agents produced abnormal and twisted mycelia, while the biocontrol agents increased mycelial branching, dilated the mycelium tip, and revealed an abnormal balloon. All of the fungicides decreased the ergosterol content, changed the cell membrane permeability, and increased the protein and nucleic acid permeability. These results suggest that these are potential agents for controlling ginseng Sclerotinia root rot disease, and their biochemical mechanisms of chemical and biocontrol of this disease were demonstrated. Full article

(This article belongs to the Special Issue Advanced Research on Biological Control of Plant Disease or Microbial Interactions (2nd Edition))

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23 pages, 3896 KiB

Open AccessArticle

Effect of Combining Wuyiencin and Pyrimethanil on Controlling Grape Gray Mold and Delaying Resistance Development in Botrytis cinerea

by Jiabei Xie, Boya Li, Jia Li, Kecheng Zhang, Longxian Ran and Beibei Ge

Microorganisms 2024, 12(7), 1383; https://doi.org/10.3390/microorganisms12071383 - 8 Jul 2024

Cited by 2 | Viewed by 1372

Abstract

By screening the compounding combination of Wuyiencin and chemical agents, this study aims to delay the emergence of chemical agent resistance, and provide a technical reference for scientific and rational fungicides technology. This study investigated the impacts of the antibiotic wuyiencin derived from Streptomyces albulus var. wuyiensis and its combination with pyrimethanil on the inhibition of Botrytis cinerea. Treatment with wuyiencin (≥80 µg mL⁻¹) strongly inhibited the pathogenicity of B. cinerea and activated the plant defense response against B. cinerea. Application of 80–100 µg mL⁻¹ wuyiencin effectively controlled grape gray mold (by 57.6–88.1% on leaves and 46.7–96.6% on fruits). Consequently, the application of 80–100 µg mL⁻¹ wuyiencin effectively mitigated grape gray mold incidence, leading to a substantial reduction in disease symptoms to nearly imperceptible levels. When wuyiencin (at the median effective concentration [EC₅₀]) was combined with pyrimethanil (EC₅₀) at a ratio of 7:3, it exhibited the highest efficacy in inhibiting B. cinerea growth. This combination was significantly more potent (p < 0.05) than using wuyiencin or pyrimethanil alone in controlling gray mold on grape leaves and fruits. Furthermore, the combination effectively delayed resistance development in gray mold. The experimental results show that wuyiencin can delay resistance development by affecting the expression of methionine biosynthesis genes and reducing the activity of the cell wall-degrading enzyme activity. Full article

(This article belongs to the Special Issue Advanced Research on Biological Control of Plant Disease or Microbial Interactions (2nd Edition))

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13 pages, 4949 KiB

Open AccessArticle

Whole Genome Sequencing Reveals Novel Insights about the Biocontrol Potential of Burkholderia ambifaria CF3 on Atractylodes lancea

by Yongxi Du, Tielin Wang, Chaogeng Lv, Binbin Yan, Xiufu Wan, Sheng Wang, Chuanzhi Kang, Lanping Guo and Luqi Huang

Microorganisms 2024, 12(6), 1043; https://doi.org/10.3390/microorganisms12061043 - 22 May 2024

Viewed by 1573

Abstract

Root rot caused by Fusarium spp. is the most destructive disease on Atractylodes lancea, one of the large bulks and most common traditional herbal plants in China. In this study, we isolated a bacterial strain, CF3, from the rhizosphere soil of A. lancea and determined its inhibitory effects on F. oxysporum in both in vitro and in vivo conditions. To deeply explore the biocontrol potential of CF3, we sequenced the whole genome and investigated the key pathways for the biosynthesis of many antibiotic compounds. The results revealed that CF3 is a member of Burkholderia ambifaria, harboring two chromosomes and one plasmid as other strains in this species. Five antibiotic compounds were found that could be synthesized due to the existence of the bio-synthesis pathways in the genome. Furthermore, the synthesis of antibiotic compounds should be confirmed by in vitro experiments and novel compounds should be purified and characterized in further studies. Full article

(This article belongs to the Special Issue Advanced Research on Biological Control of Plant Disease or Microbial Interactions (2nd Edition))

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23 pages, 11016 KiB

Open AccessArticle

Role of Volatile Organic Compounds Produced by Kosakonia cowanii Cp1 during Competitive Colonization Interaction against Pectobacterium aroidearum SM2

by Mayra Paola Mena Navarro, Merle Ariadna Espinosa Bernal, Adriana Eunice Martinez-Avila, Leonela Sofia Aponte Pineda, Luis Alberto Montes Flores, Carlos Daniel Chan Ku, Yoali Fernanda Hernández Gómez, Jacqueline González Espinosa, Juan Ramiro Pacheco Aguilar, Miguel Ángel Ramos López, Jackeline Lizzeta Arvizu Gómez, Carlos Saldaña Gutierrez, José Alberto Rodríguez Morales, Aldo Amaro Reyes, José Luis Hernández Flores and Juan Campos Guillén

Microorganisms 2024, 12(5), 930; https://doi.org/10.3390/microorganisms12050930 - 3 May 2024

Cited by 2 | Viewed by 2207

Abstract

The competitive colonization of bacteria on similar ecological niches has a significant impact during their establishment. The synthesis speeds of different chemical classes of molecules during early competitive colonization can reduce the number of competitors through metabolic effects. In this work, we demonstrate for the first time that Kosakonia cowanii Cp1 previously isolated from the seeds of Capsicum pubescens R. P. produced volatile organic compounds (VOCs) during competitive colonization against Pectobacterium aroidearum SM2, affecting soft rot symptoms in serrano chili (Capsicum annuum L.). The pathogen P. aroidearum SM2 was isolated from the fruits of C. annuum var. Serrano with soft rot symptoms. The genome of the SM2 strain carries a 5,037,920 bp chromosome with 51.46% G + C content and 4925 predicted protein-coding genes. It presents 12 genes encoding plant-cell-wall-degrading enzymes (PCDEWs), 139 genes involved in five types of secretion systems, and 16 genes related to invasion motility. Pathogenic essays showed soft rot symptoms in the fruits of C. annuum L., Solanum lycopersicum, and Physalis philadelphica and the tubers of Solanum tuberosum. During the growth phases of K. cowanii Cp1, a mix of VOCs was identified by means of HS-SPME-GC-MS. Of these compounds, 2,5-dimethyl-pyrazine showed bactericidal effects and synergy with acetoin during the competitive colonization of K. cowanii Cp1 to completely reduce soft rot symptoms. This work provides novel evidence grounding a better understanding of bacterial interactions during competitive colonization on plant tissue, where VOC synthesis is essential and has a high potential capacity to control pathogenic microorganisms in agricultural systems. Full article

(This article belongs to the Special Issue Advanced Research on Biological Control of Plant Disease or Microbial Interactions (2nd Edition))

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15 pages, 3224 KiB

Open AccessArticle

Application of Rice Straw Inhibits Clubroot Disease by Regulating the Microbial Community in Soil

by Zhe Han, Yiping Zhang, Chengqian Di, Hongwen Bi and Kai Pan

Microorganisms 2024, 12(4), 717; https://doi.org/10.3390/microorganisms12040717 - 1 Apr 2024

Viewed by 1532

Abstract

Straw return is an effective agricultural management practice for alleviating soil sickness, but only a few studies have focused on the incorporation of straw with deep plowing and rotary tillage practices in vegetable production. To determine the effects of rice straw return on Chinese cabbage clubroot, a field experiment for three consecutive years in the same area was performed. Soil microbial high-throughput sequencing, quantitative real-time polymerase chain reaction (PCR) and other methods were used to detect Chinese cabbage plant growth, clubroot occurrence, soil chemical properties and soil microbial diversity and abundance. The results showed that straw addition could significantly reduce the clubroot disease incidence. Through Illumina Miseq sequencing, the diversity of the fungi decreased obviously. The relative abundance of the phyla Proteobacteria and Firmicutes was strikingly reduced, while that of Chloroflexi was significantly increased. Redundancy analysis suggests that soil properties may also affect the soil microbial composition; changes in the microbial structure of bacteria and fungi were associated with the available phosphorus. In conclusion, the continuous addition of rice straw can promote the growth and control the occurrence of clubroot, which is closely related to the microbial composition, and the inhibition effect is proportional to the age of addition. Full article

(This article belongs to the Special Issue Advanced Research on Biological Control of Plant Disease or Microbial Interactions (2nd Edition))

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13 pages, 5366 KiB

Open AccessArticle

Effects of 2-Phenylethanol on Controlling the Development of Fusarium graminearum in Wheat

by Shufang Sun, Nawen Tang, Kun Han, Qunqing Wang and Qian Xu

Microorganisms 2023, 11(12), 2954; https://doi.org/10.3390/microorganisms11122954 - 10 Dec 2023

Cited by 6 | Viewed by 1867

Abstract

Applying plant-derived fungicides is a safe and sustainable way to control wheat scab. In this study, volatile organic compounds (VOCs) of wheat cultivars with and without the resistance gene Fhb1 were analyzed by GC-MS, and 2-phenylethanol was screened out. The biocontrol function of 2-phenylethanol on Fusarium graminearum was evaluated in vitro and in vivo. Metabolomics analysis indicated that 2-phenylethanol altered the amino acid pathways of F. graminearum, affecting its normal life activities. Under SEM and TEM observation, the mycelial morphology changed, and the integrity of the cell membrane was destroyed. Furthermore, 2-phenylethanol could inhibit the production of mycotoxins (DON, 3-ADON, 15-ADON) by F. graminearum and reduce grain contamination. This research provides new ideas for green prevention and control of wheat FHB in the field. Full article

(This article belongs to the Special Issue Advanced Research on Biological Control of Plant Disease or Microbial Interactions (2nd Edition))

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20 pages, 3597 KiB

Open AccessArticle

Avirulent Isolates of Penicillium chrysogenum to Control the Blue Mold of Apple Caused by P. expansum

by Holly P. Bartholomew, Dianiris Luciano-Rosario, Michael J. Bradshaw, Verneta L. Gaskins, Hui Peng, Jorge M. Fonseca and Wayne M. Jurick II

Microorganisms 2023, 11(11), 2792; https://doi.org/10.3390/microorganisms11112792 - 17 Nov 2023

Cited by 3 | Viewed by 2149

Abstract

Blue mold is an economically significant postharvest disease of pome fruit that is primarily caused by Penicillium expansum. To manage this disease and sustain product quality, novel decay intervention strategies are needed that also maintain long-term efficacy. Biocontrol organisms and natural products are promising tools for managing postharvest diseases. Here, two Penicillium chrysogenum isolates, 404 and 413, were investigated as potential biocontrol agents against P. expansum in apple. Notably, 404 and 413 were non-pathogenic in apple, yet they grew vigorously in vitro when compared to the highly aggressive P. expansum R19 and Pe21 isolates. Whole-genome sequencing and species-specific barcoding identified both strains as P. chrysogenum. Each P. chrysogenum strain was inoculated in apple with the subsequent co-inoculation of R19 or Pe21 simultaneously, 3, or 7 days after prior inoculation with 404 or 413. The co-inoculation of these isolates showed reduced decay incidence and severity, with the most significant reduction from the longer establishment of P. chrysogenum. In vitro growth showed no antagonism between species, further suggesting competitive niche colonization as the mode of action for decay reduction. Both P. chrysogenum isolates had incomplete patulin gene clusters but tolerated patulin treatment. Finally, hygromycin resistance was observed for both P. chrysogenum isolates, yet they are not multiresistant to apple postharvest fungicides. Overall, we demonstrate the translative potential of P. chrysogenum to serve as an effective biocontrol agent against blue mold decay in apples, pending practical optimization and formulation. Full article

(This article belongs to the Special Issue Advanced Research on Biological Control of Plant Disease or Microbial Interactions (2nd Edition))

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10 pages, 1679 KiB

Open AccessBrief Report

Evaluating the Role of Viable Cells, Heat-Killed Cells or Cell-Free Supernatants in Bacterial Biocontrol of Fungi: A Comparison Between Lactic Acid Bacteria and Pseudomonas

by Francesca Di Rico, Francesco Vuolo and Edoardo Puglisi

Microorganisms 2025, 13(1), 105; https://doi.org/10.3390/microorganisms13010105 - 7 Jan 2025

Cited by 1 | Viewed by 945

Abstract

This study investigated whether viable cells, dead cells or cell-free supernatants (CFS) were responsible for the biocontrol effect of strains from two important bacterial genera, Pseudomonas and Lactobacillus, known for their antifungal properties against plant pathogens and food spoilage microorganisms. Specifically, the capability of these strains to produce extracellular hydrolytic enzymes on specified media was assessed, along with their effectiveness in inhibiting the mycelial growth of several phytopathogenic fungi (Fusarium oxysporum, Botrytis cinerea, Pythium ultimum and Rhizoctonia solani) using dual culture plate assays. Results from these inhibition assays revealed that P. fluorescens PF05 and L. plantarum LMG 23520 strains were the most effective in suppressing fungal growth, especially F. oxysporum. Therefore, further experiments were carried out to investigate the antifungal potential of the viable cells, heat-killed cells (HKC) and CFS from these strains against the germination of F. oxysporum spores. The viable cell trial proved successful, whereas HKC from the two bacterial isolates were ineffective against fungal spore germination. Conversely, the CFS of L. plantarum LMG 23520 was able to prevent fungal spore development for up to six days. The CFS of P. fluorescens PF05, instead, did not yield positive results. Additional studies are required to evaluate the potential inhibitory effects of the CFS from P. fluorescens PF05 and the HKC from both strains. Full article

(This article belongs to the Special Issue Advanced Research on Biological Control of Plant Disease or Microbial Interactions (2nd Edition))

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