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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 (30 September 2023) | Viewed by 18841

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Dr. Sabrina Sarrocco

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Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
Interests: plant pathogenic fungi; mycotoxigenic fungi; biocontrol fungi; fungal ecology; fungal secondary metabolites; fungal genome editing
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Dr. Isabel Vicente

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Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
Interests: plant pathology; biocontrol; fungi; secondary metabolites; molecular fungal interactions; Trichoderma
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Special Issue Information

Dear Colleagues,

Fungi are one of the most ecologically successful groups of organisms due to their ability to colonize any environment. Some phytopathogenic fungi feed on a broad range of host plants, exploiting generalist traits often combined with strong competition strategies. Other fungi develop specialized mechanisms of plant infection and colonization that involve host-specific virulence factors. Environmental challenges shape fungal genomes, and their plasticity results in the evolution of novel traits for niche adaptation and plant disease establishment. Comparative genomics and genetic engineering expand the limits of basic research towards in-field approaches based on the development of more efficient tools for pathogen detection and disease management.

In this Special Issue of Microorganisms, the topics will include, but are not limited to:

Fungal effectors;
Secondary metabolites involved in plant colonization and fungal pathogenesis;
Genomics and evolution of plant-pathogenic fungi;
Novel patho-systems;
Innovative tools for the early detection and management of fungal diseases on plants.

Dr. Sabrina Sarrocco
Dr. Isabel Vicente
Guest Editors

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Keywords

fungal effectors
plant pathogens
fungal genomics
fungal evolution
fungal ecology
plant disease management

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Published Papers (10 papers)

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Research

20 pages, 5168 KiB

Open AccessArticle

Identification of Fungicide Combinations for Overcoming Plasmopara viticola and Botrytis cinerea Fungicide Resistance

by Junrui Zhang, Jhulia Gelain, Guido Schnabel, Samavath Mallawarachchi, Haoqi Wang, Nirmitee Mulgaonkar, Raghupathy Karthikeyan and Sandun Fernando

Microorganisms 2023, 11(12), 2966; https://doi.org/10.3390/microorganisms11122966 - 12 Dec 2023

Cited by 2 | Viewed by 1316

Abstract

Fungal diseases, including downy mildew (caused by Plasmopara viticola) and gray mold (caused by Botrytis cinerea), significantly impact the marketable yield of grapes produced worldwide. Cytochrome b of the mitochondrial respiratory chain of these two fungi is a key target for Quinone outside inhibitor (QoI)-based fungicide development. Since the mode of action (MOA) of QoI fungicides is restricted to a single site, the extensive usage of these fungicides has resulted in fungicide resistance. The use of fungicide combinations with multiple targets is an effective way to counter and slow down the development of fungicide resistance. Due to the high cost of in planta trials, in silico techniques can be used for the rapid screening of potential fungicides. In this study, a combination of in silico simulations that include Schrödinger Glide docking, molecular dynamics, and Molecular Mechanism-Generalized Born Surface Area calculation were used to screen the most potent QoI and non-QoI-based fungicide combinations to wild-type, G143A-mutated, F129L-mutated, and double-mutated versions that had both G143A and F129L mutations of fungal cytochrome b. In silico docking studies indicated that mandestrobin, famoxadone, captan, and thiram have a high affinity toward WT cytochrome b of Botrytis cinerea. Although the QoIs mandestrobin and famoxadone were effective for WT based on in vitro results, they were not broadly effective against G143A-mutated isolates. Famoxadone was only effective against one isolate with G143A-mutated cytochrome b. The non-QoI fungicides thiram and captan were effective against both WT and isolates with G143A-mutated cytochrome b. Follow-up in silico docking and molecular dynamics studies suggested that fungicide combinations consisting of famoxadone, mandestrobin, fenamidone, and thiram should be considered in field testing targeting Plasmopara viticola and Botrytis cinerea fungicide resistance. Full article

(This article belongs to the Special Issue Plant-Pathogenic Fungi)

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12 pages, 1646 KiB

Open AccessArticle

The SIX5 Protein in Fusarium oxysporum f. sp. cepae Acts as an Avirulence Effector toward Shallot (Allium cepa L. Aggregatum Group)

by Kosei Sakane, Masaaki Kunimoto, Kazuki Furumoto, Masayoshi Shigyo, Kazunori Sasaki and Shin-ichi Ito

Microorganisms 2023, 11(12), 2861; https://doi.org/10.3390/microorganisms11122861 - 26 Nov 2023

Viewed by 1411

Abstract

Fusarium oxysporum f. sp. cepae (Foc) causes basal rot disease in Allium species, including onions (Allium cepa L.) and shallots (A. cepa L. Aggregatum group). Among Allium species, shallots can be crossbred with onions and are relatively more resistant to Foc than onions. Thus, shallots are considered a potential disease-resistant resource for onions. However, the mechanisms underlying the molecular interactions between shallots and Foc remain unclear. This study demonstrated that SIX5, an effector derived from Foc (FocSIX5), acts as an avirulence effector in shallots. We achieved this by generating a FocSIX5 gene knockout mutant in Foc, for which experiments which revealed that it caused more severe wilt symptoms in Foc-resistant shallots than the wild-type Foc and FocSIX5 gene complementation mutants. Moreover, we demonstrated that a single amino acid substitution (R67K) in FocSIX5 was insufficient to overcome shallot resistance to Foc. Full article

(This article belongs to the Special Issue Plant-Pathogenic Fungi)

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12 pages, 1657 KiB

Open AccessArticle

Molecular Characterization of Ciborinia camelliae Kohn Shows Intraspecific Variability and Suggests Transcontinental Movement of the Pathogen

by Marco Saracchi, Irene Valenti, Paolo Cortesi, Daniela Bulgari, Andrea Kunova and Matias Pasquali

Microorganisms 2023, 11(11), 2727; https://doi.org/10.3390/microorganisms11112727 - 8 Nov 2023

Viewed by 1065

Abstract

Ciborinia camelliae Kohn is the causal agent of camellia flower blight. The fungus infects only the flowers of camellias. C. camelliae isolates obtained from symptomatic samples, collected in 13 different localities worldwide, were characterized by Multi-Locus Sequence Typing (MLST) using the following: (i) a nuclear ribosomal DNA internal transcribed spacer; (ii) subunit 2 of β-tubulin (β-TUB II), (iii) elongation factor 1-α (EF1α); and (iv) glycerol-3-phosphate dehydrogenase (GPDH). The variability of the strains was assessed using a universally primed–polymerase chain reaction (UP-PCR) with six universal primers. Gene sequence comparison showed high similarity among all the European strains and highlighted the diversity of the New Zealand and Chinese representative strains. The profiles obtained by UP-PCR confirmed the significant diversity of extra-European strains and identified subgroups within the European population. The presence of shared genetic profiles obtained from strains isolated in different countries (New Zealand and France) suggests the movement of strains from one location to another, which is probably due to the exchange of infected plant material. Moreover, our study shows the overall high intraspecific variability of C. camelliae, which is likely due to the sexual reproduction of the fungus, suggesting the risk of emergence of new pathotypes adapting to novel camellia varieties. Full article

(This article belongs to the Special Issue Plant-Pathogenic Fungi)

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14 pages, 2481 KiB

Open AccessArticle

Plant Growth-Promoting Endophytic Bacteria Isolated from Miscanthus giganteus and Their Antifungal Activity

by Petra Lovecká, Gabriela Kroneislová, Zuzana Novotná, Jana Röderová and Kateřina Demnerová

Microorganisms 2023, 11(11), 2710; https://doi.org/10.3390/microorganisms11112710 - 5 Nov 2023

Cited by 1 | Viewed by 2265

Abstract

Modern technologies can satisfy human needs only with the use of large quantities of fertilizers and pesticides that are harmful to the environment. For this reason, it is possible to develop new technologies for sustainable agriculture. The process could be carried out by using endophytic microorganisms with a (possible) positive effect on plant vitality. Bacterial endophytes have been reported as plant growth promoters in several kinds of plants under normal and stressful conditions. In this study, isolates of bacterial endophytes from the roots and leaves of Miscanthus giganteus plants were tested for the presence of plant growth-promoting properties and their ability to inhibit pathogens of fungal origin. Selected bacterial isolates were able to solubilize inorganic phosphorus, fix nitrogen, and produce phytohormones, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, and siderophore. Leaf bacterial isolate Pantoea ananat is 50 OL 2 had high production of siderophores (zone ≥ 5 mm), and limited phytohormone production, and was the only one to show ACC deaminase activity. The root bacterial isolate of Pseudomonas libanensis 5 OK 7A showed the best results in phytohormone production (N6-(Δ2-isopentenyl)adenine and indole-3-acetic acid, 11.7 and 12.6 ng·mL⁻¹, respectively). Four fungal cultures—Fusarium sporotrichioides DBM 4330, Sclerotinia sclerotiorum SS-1, Botrytis cinerea DS 90 and Sphaerodes fimicola DS 93—were used to test the antifungal activity of selected bacterial isolates. These fungal cultures represent pathogenic families, especially for crops. All selected root endophyte isolates inhibited the pathogenic growth of all tested fungi with inhibition percentages ranging from 30 to 60%. Antifungal activity was also tested in two forms of immobilization of selected bacterial isolates: one in agar and the other on dextrin-coated cellulose carriers. These results demonstrated that the endophytic Pseudomonas sp. could be used as biofertilizers for crops. Full article

(This article belongs to the Special Issue Plant-Pathogenic Fungi)

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23 pages, 5789 KiB

Open AccessArticle

The Mechanism of Transcription Factor Swi6 in Regulating Growth and Pathogenicity of Ceratocystis fimbriata: Insights from Non-Targeted Metabolomics

by Hao Cong, Changgen Li, Yiming Wang, Yongjing Zhang, Daifu Ma, Lianwei Li and Jihong Jiang

Microorganisms 2023, 11(11), 2666; https://doi.org/10.3390/microorganisms11112666 - 30 Oct 2023

Cited by 3 | Viewed by 1755

Abstract

Ceratocystis fimbriata (C. fimbriata) is a notorious pathogenic fungus that causes sweet potato black rot disease. The APSES transcription factor Swi6 in fungi is located downstream of the cell wall integrity (CWI)-mitogen-activated protein kinase (MAPK) signaling pathway and has been identified to be involved in cell wall integrity and virulence in several filamentous pathogenic fungi. However, the specific mechanisms by which Swi6 regulates the growth and pathogenicity of plant pathogenic fungi remain elusive. In this study, the SWI6 deletion mutants and complemented strains of C. fimbriata were generated. Deletion of Swi6 in C. fimbriata resulted in aberrant growth patterns. Pathogenicity assays on sweet potato storage roots revealed a significant decrease in virulence in the mutant. Non-targeted metabolomic analysis using LC-MS identified a total of 692 potential differentially accumulated metabolites (PDAMs) in the ∆Cfswi6 mutant compared to the wild type, and the results of KEGG enrichment analysis demonstrated significant enrichment of PDAMs within various metabolic pathways, including amino acid metabolism, lipid metabolism, nucleotide metabolism, GPI-anchored protein synthesis, and ABC transporter metabolism. These metabolic pathways were believed to play a crucial role in mediating the growth and pathogenicity of C. fimbriata through the regulation of CWI. Firstly, the deletion of the SWI6 gene led to abnormal amino acid and lipid metabolism, potentially exacerbating energy storage imbalance. Secondly, significant enrichment of metabolites related to GPI-anchored protein biosynthesis implied compromised cell wall integrity. Lastly, disruption of ABC transport protein metabolism may hinder intracellular transmembrane transport. Importantly, this study represents the first investigation into the potential regulatory mechanisms of SWI6 in plant filamentous pathogenic fungi from a metabolic perspective. The findings provide novel insights into the role of SWI6 in the growth and virulence of C. fimbriata, highlighting its potential as a target for controlling this pathogen. Full article

(This article belongs to the Special Issue Plant-Pathogenic Fungi)

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14 pages, 5705 KiB

Open AccessArticle

Natural Product Aloesin Significantly Inhibits Spore Germination and Appressorium Formation in Magnaporthe oryzae

by Guohui Zhang, Rongyu Li, Xiaomao Wu and Ming Li

Microorganisms 2023, 11(10), 2395; https://doi.org/10.3390/microorganisms11102395 - 26 Sep 2023

Cited by 1 | Viewed by 1378

Abstract

This study aims to determine the effects of the natural product aloesin against Magnaporthe oryzae. The results exposed that aloesin had a high inhibitory effect on appressorium formation (the EC₅₀ value was 175.26 μg/mL). Microscopic examination revealed that 92.30 ± 4.26% of M. oryzae spores could be broken down by 625.00 μg/mL of aloesin, and the formation rate of appressoria was 4.74 ± 1.00% after 12 h. M. oryzae mycelial growth was weaker than that on the control. The enzyme activity analysis results indicated that aloesin inhibited the activities of polyketolase (PKS), laccase (LAC), and chain-shortening catalytic enzyme (Aayg1), which are key enzymes in melanin synthesis. The inhibition rate by aloesin of PKS, LAC, and Aayg1 activity was 32.51%, 33.04%, and 43.38%, respectively. The proteomic analysis showed that actin expression was downregulated at 175.62 μg/mL of aloesin, which could reduce actin bundle formation and prevent the polar growth of hyphae in M. oryzae. This is the first report showing that aloesin effectively inhibits conidia morphology and appressorium formation in M. oryzae. Full article

(This article belongs to the Special Issue Plant-Pathogenic Fungi)

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16 pages, 10726 KiB

Open AccessArticle

The Impact of the Soil Survival of the Pathogen of Fusarium Wilt on Soil Nutrient Cycling Mediated by Microorganisms

by Xuecheng Yan, Shuhan Guo, Kexiang Gao, Shuaibin Sun, Chenglin Yin and Yehan Tian

Microorganisms 2023, 11(9), 2207; https://doi.org/10.3390/microorganisms11092207 - 31 Aug 2023

Cited by 4 | Viewed by 2177

Abstract

Fusarium wilt of Momordica charantia in the greenhouse is one of the most severe crop diseases in Shandong Province, P.R. China. This study aimed to investigate the mechanisms of accumulation and long-term survival of the pathogen in naturally pathogenic soils. Soil physicochemical properties were tested after applying a highly virulent strain of Fusarium wilt to M. charantia in an artificial disease nursery. The functional structure of soil microorganisms was analyzed through amplicon sequencing. The highly virulent strain SG−15 of F. oxysporum f. sp. momordicae was found to cause Fusarium wilt in M. charantia in Shandong Province. The strain SG−15 could not infect 14 non-host crops, including Solanum melongena and Lycopersicon esculentum, but it had varying degrees of pathogenicity towards 11 M. charantia varieties. In the artificial disease nursery for Fusarium wilt of M. charantia, the F. oxysporum was distributed in the soil to a depth of 0–40 cm and was mainly distributed in crop residues at 0–10 cm depth. During crop growth, F. oxysporum primarily grows and reproduces in susceptible host plants, rather than disease-resistant hosts and non-host crops. The colonization of the pathogen of Fusarium wilt significantly changed the soil physicochemical properties, the functional structure of soil microorganisms and the circulation of soil elements such as carbon, nitrogen, phosphorus and sulfur. Soil pH value, organic matter content, available iron content, available manganese content, FDA hydrolase activity and polyphenol oxidase activity were significantly correlated with the relative abundance of Fusarium wilt pathogens in the soil. In general, this study suggests that susceptible host plants facilitate the accumulation of Fusarium wilt pathogens in the soil. These pathogens can mediate the decomposition process of plant residues, particularly those of diseased plants, and indirectly or directly affect soil’s chemical properties. Full article

(This article belongs to the Special Issue Plant-Pathogenic Fungi)

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21 pages, 3479 KiB

Open AccessArticle

A New Proposed Symbiotic Plant–Herbivore Relationship between Burkea africana Trees, Cirina forda Caterpillars and Their Associated Fungi Pleurostomophora richardsiae and Aspergillus nomius

by Lufuno Ethel Nemadodzi and Gerhard Prinsloo

Microorganisms 2023, 11(7), 1864; https://doi.org/10.3390/microorganisms11071864 - 24 Jul 2023

Cited by 1 | Viewed by 1586

Abstract

Burkea africana is a tree found in savannah and woodland in southern Africa, as well as northwards into tropical African regions as far as Nigeria and Ethiopia. It is used as fuel wood, medicinally to treat various conditions, such as toothache, headache, migraine, pain, inflammation, and sexually transmitted diseases, such as gonorrhoea, but also an ornamental tree. The current study investigated the possible symbiotic relationship between B. africana trees and the C. forda caterpillars and the mutual role played in ensuring the survival of B. africana trees/seedlings in harsh natural conditions and low-nutrient soils. Deoxyribonucleic acid isolation and sequencing results revealed that the fungal species Pleurostomophora richardsiae was highly predominant in the leaves of B. africana trees and present in the caterpillars. The second most prominent fungal species in the caterpillars was Aspergillus nomius. The latter is known to be related to a Penicillium sp. which was found to be highly prevalent in the soil where B. africana trees grow and is suggested to play a role in enhancing the effective growth of B. africana trees in their natural habitat. To support this, a phylogenetic analysis was conducted, and a tree was constructed, which shows a high percentage similarity between Aspergillus and Penicillium sp. The findings of the study revealed that B. africana trees not only serve as a source of feed for the C. forda caterpillar but benefit from C. forda caterpillars which, after dropping onto the soil, is proposed to inoculate the soil surrounding the trees with the fungus A. nomius which suggests a symbiotic and/or synergistic relationship between B. africana trees and C. forda caterpillars. Full article

(This article belongs to the Special Issue Plant-Pathogenic Fungi)

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17 pages, 3244 KiB

Open AccessArticle

Insights on Novel Effectors and Characterization of Metacaspase (RS107_6) as a Potential Cell Death-Inducing Protein in Rhizoctonia solani

by N. Kavya, M. K. Prasannakumar, Gopal Venkateshbabu, Vidya Niranjan, Akshay Uttarkar, P. Buela Parivallal, Sahana N. Banakar, H. B. Mahesh, Pramesh Devanna, K. G. Manasa and Tagginahalli N. Shivakumara

Microorganisms 2023, 11(4), 920; https://doi.org/10.3390/microorganisms11040920 - 1 Apr 2023

Cited by 3 | Viewed by 1928

Abstract

Effectors play an important role in host–pathogen interactions. Though an economically significant disease in rice, knowledge regarding the infection strategy of Rhizoctonia solani is obscure. In this study, we performed a genome-wide identification of the effectors in R. solani based on the characteristics of previously reported effector proteins. A total of seven novel effectors (designated as RS107_1 to RS107_7) in the disease mechanism of R. solani were identified and were predicted to be non-classically secreted proteins with functionally conserved domains. The function, reactivity, and stability of these proteins were evaluated through physiochemical characterization. The target proteins involved in the regulation of rice defense mechanisms were identified. Furthermore, the effector genes were cloned and RS107_6 (metacaspase) was heterologously expressed in Escherichia coli to obtain a purified protein of ~36.5 kDa. The MALD-TOF characterization confirmed that the protein belonged to a metacaspase of the Peptidase_C14 protein family, 906 bp in size, and encoded a polypeptide of 301 amino acids. These findings suggest that the identified effectors can potentially serve as a virulence factor and can be targeted for the management of sheath blight in rice. Full article

(This article belongs to the Special Issue Plant-Pathogenic Fungi)

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17 pages, 4091 KiB

Open AccessArticle

Comparative Penicillium spp. Transcriptomics: Conserved Pathways and Processes Revealed in Ungerminated Conidia and during Postharvest Apple Fruit Decay

by Holly P. Bartholomew, Franz J. Lichtner, Michael Bradshaw, Verneta L. Gaskins, Jorge M. Fonseca, Joan W. Bennett and Wayne M. Jurick II

Microorganisms 2022, 10(12), 2414; https://doi.org/10.3390/microorganisms10122414 - 6 Dec 2022

Cited by 6 | Viewed by 2623

Abstract

Blue mold, caused by Penicillium spp., is an impactful postharvest disease resulting in significant economic losses due to reduced pome fruit quality and mycotoxin contamination. Using two Penicillium species with different levels of aggressiveness, transcriptomics were implemented in order to identify genes expressed during apple fruit decay and loci expressed in ungerminated conidia. Total RNA was isolated from ungerminated conidia and decayed apple fruit infected with P. expansum R19 or P. polonicum RS1. There were 2442 differentially expressed genes (DEGs) between the R19 and RS1 in apple. Comparisons within species between apple and conidia revealed 4404 DEGs for R19 and 2935 for RS1, respectively. Gene ontology (GO) analysis revealed differential regulation in fungal transport and metabolism genes during decay, suggesting a flux in nutrient acquisition and detoxification strategies. In R19, the oxidoreductase GO category comprised 20% of all DEG groups in apple verses conidia. Ungerminated conidia from both species showed DEGs encoding the glyoxylate shunt and beta-oxidation, specifying the earliest metabolic requirements for germination. This is the first study to identify pre-loaded transcripts in conidia from blue mold fungi, reveal unique genes between species expressed during apple decay, and show the expression dynamics of known fungal virulence factors. These findings will enable development of targeted approaches for blue mold abatement strategies. Full article

(This article belongs to the Special Issue Plant-Pathogenic Fungi)

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