An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Muggia, Lucía; Ametrano, Claudio Gennaro; Sterflinger, Katja; Tesei, Donatella

doi:10.3390/life10120356

Cited by 16 publications

(10 citation statements)

References 412 publications

(630 reference statements)

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“…They can adapt to a wide range of substrates in challenging environments such as ultraviolet light, water and high temperature stress [ 23 ]. Ascomycota has been shown to be pathogenic fungi in plants and insects [ 24 ]. However, Mycosphaerella was dominant in non-bagging group at the beginning of the storage period which was significantly different from the bagging group.…”

Section: Discussionmentioning

confidence: 99%

Fruit bagging reduces the postharvest decay and alters the diversity of fruit surface fungal community in ‘Yali’ pear

Gao

Zhang

et al. 2022

BMC Microbiol

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Background Fruit bagging is an effective technique for fruit protection in the orchard management. Bagging can create a micro-environment for fruit growth and affect fruit quality during storage, in which the diversity of microorganisms may play an important role. Therefore, various methods including biochemistry, analytical chemistry, and bioinformatics methods were used to reveal the influences of fruit bagging on postharvest fruit quality, physiological characters, decay and surface fungal community of ‘Yali’ pear fruit were investigated in this study. Results Fruit bagging significantly decreased the postharvest decay after 15 days of ambient storage. There were no significant differences in fruit firmness, titratable acid and ethylene production rate between the fruit-bagging and non-bagging group after 15 days of storage, while the soluble solids contents (SSC) and respiration rate in non-bagging fruit was significantly higher than that in fruit-bagging after 15 days of storage. Furthermore, the surface microbes of pear were collected and determined by the new generation sequencing technology. The alpha diversity of fungi in non-bagging fruit decreased significantly after 15 days of storage, while there were no significant changes in bagging fruit. Ascomycota and Basidiomycota were the two major phyla detected in the bagging fruit, and the dominant fungal genera were Alternaria (23.7%), Mycosphaerella (17.25%), Vishniacozyma (16.14%), and Aureobasidium (10.51%) after 15 days of storage. For the non-bagging pear, Ascomycota was the only phylum detected, and the dominant genera was Pichia (83.32%) after 15 days of storage. The abundance of Pichia may be regarded as the biomarker to indicate the degree of fruit decay. Conclusions This study showed that fruit bagging could significantly reduce postharvest fruit decay and respiration rate of ‘Yali’ pear. Significant differences were found in fungal composition between bagging and non-bagging pear after storage for 0 or 15 days. Fruit bagging maintained the diversity of fungi on the fruit surface, increased the abundance of non-pathogenic fungi, and even antagonistic fungi such as Aureobasidium, Vishniacozyma, and Mycosphaerella. A reduction in the abundance of pathogenic fungi and incidence of postharvest decay during the storage of ‘Yali’ pear were also recorded. In conclusion, fruit-bagging changed the fungal diversity on fruit surface of ‘Yali’ pear, which had significant effect on reducing postharvest fruit decay, and thus prolong the storage period of ‘Yali’ pears. The future thrust of this study will focus on the isolation of fungi or bacteria from pear fruit surface and identify their roles in causing fruit decay and changing fruit quality during storage.

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Section: Discussionmentioning

confidence: 99%

Fruit bagging reduces the postharvest decay and alters the diversity of fruit surface fungal community in ‘Yali’ pear

Gao

Zhang

et al. 2022

BMC Microbiol

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“…Furthermore, when compared to the control, it was observed that B4-7 significantly increased the abundance of Firmicutes and Mortierellomycota, while significantly reducing the abundance of Ascomycota and Basidiomycota. Additionally, studies have indicated that Ascomycota and Basidiomycota are known to include plant and insect pathogenic fungi ( Muggia et al., 2020 ). Mortierellomycota contributes to the decomposition of organic matter and cellulose in soil, providing nutrients for plant growth ( Purahong et al., 2016 ).…”

Section: Discussionmentioning

confidence: 99%

Screening, identification and evaluation of an acidophilic strain of Bacillus velezensis B4-7 for the biocontrol of tobacco bacterial wilt

Meng,

Wang,

et al. 2024

Front. Plant Sci.

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Tobacco (Nicotiana tabacum L.) bacterial wilt, caused by Ralstonia solanacearum, is indeed a highly destructive plant disease, leading to substantial damage in tobacco production. While biological control is considered an effective measure for managing bacterial wilt, related research in this area has been relatively limited compared to other control methods. In order to discover new potential antagonistic bacteria with high biocontrol efficacy against tobacco bacterial wilt, we conducted an analysis of the microbial composition differences between disease-suppressive and disease-conducive soils using Illumina sequencing. As a result, we successfully isolated six strains from the disease-suppressive soil that exhibited antibacterial activity against Ralstonia solanacearum. Among these strains, B4-7 showed the strongest antibacterial activity, even at acidic conditions with a pH of 4.0. Based on genome analysis using Average Nucleotide Identity (ANI), B4-7 was identified as Bacillus velezensis. In greenhouse and field trials, strain B4-7 significantly reduced the disease index of tobacco bacterial wilt, with control efficiencies reaching 74.03% and 46.88% respectively. Additionally, B4-7 exhibited plant-promoting abilities that led to a 35.27% increase in tobacco production in field conditions. Quantitative real-time (qPCR) analysis demonstrated that strain B4-7 effectively reduced the abundance of R. solanacearum in the rhizosphere. Genome sequencing and Liquid Chromatography-Mass Spectrometry (LC-MS) analysis revealed that strain B4-7 potentially produces various lipopeptide metabolites, such as microlactin, bacillaene, difficidin, bacilysin, and surfactin. Furthermore, B4-7 influenced the structure of the rhizosphere soil microbial community, increasing bacterial abundance and fungal diversity, while also promoting the growth of different beneficial microorganisms. In addition, B4-7 enhanced tobacco’s resistance to R. solanacearum by increasing the activities of defense enzymes, including superoxide dismutase (SOD), phenylalanine ammonia-lyase (PAL), peroxidase (POD), catalase (CAT), and polyphenol oxidase (PPO). Collectively, these findings suggest that B. velezensis B4-7 holds significant biocontrol potential and can be considered a promising candidate strain for eco-friendly management of tobacco bacterial wilt.

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“…The ability of microorganisms to survive and proliferate in extreme environments is facilitated by numerous characteristics; chief among them is their capacity to withstand the competition and stress presented by their natural habitats 1 , 2 . These microorganisms are capable of adapting to both physical and chemical stressors via phenotypic plasticity 3 , 4 .…”

Section: Introductionmentioning

confidence: 99%

Genomic and morphological characterization of Knufia obscura isolated from the Mars 2020 spacecraft assembly facility

Chander,

de Melo Teixeira,

Singh

et al. 2024

Sci Rep

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Members of the family Trichomeriaceae, belonging to the Chaetothyriales order and the Ascomycota phylum, are known for their capability to inhabit hostile environments characterized by extreme temperatures, oligotrophic conditions, drought, or presence of toxic compounds. The genus Knufia encompasses many polyextremophilic species. In this report, the genomic and morphological features of the strain FJI-L2-BK-P2 presented, which was isolated from the Mars 2020 mission spacecraft assembly facility located at the Jet Propulsion Laboratory in Pasadena, California. The identification is based on sequence alignment for marker genes, multi-locus sequence analysis, and whole genome sequence phylogeny. The morphological features were studied using a diverse range of microscopic techniques (bright field, phase contrast, differential interference contrast and scanning electron microscopy). The phylogenetic marker genes of the strain FJI-L2-BK-P2 exhibited highest similarities with type strain of Knufia obscura (CBS 148926T) that was isolated from the gas tank of a car in Italy. To validate the species identity, whole genomes of both strains (FJI-L2-BK-P2 and CBS 148926T) were sequenced, annotated, and strain FJI-L2-BK-P2 was confirmed as K. obscura. The morphological analysis and description of the genomic characteristics of K. obscura FJI-L2-BK-P2 may contribute to refining the taxonomy of Knufia species. Key morphological features are reported in this K. obscura strain, resembling microsclerotia and chlamydospore-like propagules. These features known to be characteristic features in black fungi which could potentially facilitate their adaptation to harsh environments.

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An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Cited by 16 publications

References 412 publications

Fruit bagging reduces the postharvest decay and alters the diversity of fruit surface fungal community in ‘Yali’ pear

Fruit bagging reduces the postharvest decay and alters the diversity of fruit surface fungal community in ‘Yali’ pear

Screening, identification and evaluation of an acidophilic strain of Bacillus velezensis B4-7 for the biocontrol of tobacco bacterial wilt

Genomic and morphological characterization of Knufia obscura isolated from the Mars 2020 spacecraft assembly facility

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