| 1. |
- Casini, Giulia, et al.
(författare)
-
Endophytic fungal communities of ancient wheat varieties
- 2019
-
Ingår i: Phytopathologia Mediterranea. - 0031-9465. ; 58:1, s. 151-162
-
Tidskriftsartikel (refereegranskat)abstract
- The fungal community composition and structure of two ancient tetraploid wheat varieties, native to the Sicilian territory of Italy, Perciasacchi (winter wheat) and Tumminia (spring wheat) were investigated using High Throughput Sequencing (HTS). This showed a predominance of Ascomycetes and Basidiomycetes including Alternaria, Fusarium, Mycosphaerella, Filobasidium, Cystofilobasidium, Cryptococcus, Leucosporidium, Dioszegia, Puccinia, Sporobolomyces, Aureobasidium, Cladosporium, Holtermanniella and Gibberella. Principal Coordinates Analysis (PCoA) and Linear discriminant analysis Effect Size (LEfSe) showed that Aureobasidium, Leucosporidium and Puccinia differentiated between the two wheat varieties. In addition, the microbial association analysis suggested that some endophytic taxa play important roles within the wheat fungal community. Genera such as Cryptococcus and Cystofilobasidium were shown to have consistent antagonistic activity against Gibberella spp., while, Acremonium and a group of unidentified ascomycetes had mutual exclusion relationships with Puccinia. Since both Gibberella and Puccinia contain several economically important pathogens of wheat, the detected fungal interactions may indicate microbial-mediated resistance in these wheat varieties.
|
|
| 2. |
- Abdelfattah, Ahmed, et al.
(författare)
-
Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root
- 2021
-
Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 23:4, s. 2199-2214
-
Tidskriftsartikel (refereegranskat)abstract
- While the environment is considered the primary origin of the plant microbiome, the potential role of seeds as a source of transmitting microorganisms has not received much attention. Here we tested the hypothesis that the plant microbiome is partially inherited through vertical transmission. An experimental culturing device was constructed to grow oak seedlings in a microbe-free environment while keeping belowground and aboveground tissues separated. The microbial communities associated with the acorn's embryo and pericarp and the developing seeding's phyllosphere and root systems were analysed using amplicon sequencing of fungal ITS and bacterial 16S rDNA. Results showed that the seed microbiome is diverse and non-randomly distributed within an acorn. The microbial composition of the phyllosphere was diverse and strongly resembled the composition found in the embryo, whereas the roots and pericarp each had a less diverse and distinct microbial community. Our findings demonstrate a high level of microbial diversity and spatial partitioning of the fungal and bacterial community within both seed and seedling, indicating inheritance, niche differentiation and divergent transmission routes for the establishment of root and phyllosphere communities.
|
|
| 3. |
- Abdelfattah, Ahmed, et al.
(författare)
-
Impact of Bactrocera oleae on the fungal microbiota of ripe olive drupes
- 2018
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 13:11
-
Tidskriftsartikel (refereegranskat)abstract
- The olive fruit fly (OFF), Bactrocera oleae is the most devastating pest affecting olive fruit worldwide. Previous investigations have addressed the fungal microbiome associated with olive drupes or B. oleae, but the impact of the insect on fungal communities of olive fruit remains undescribed. In the present work, the fungal microbiome of olive drupes, infested and non-infested by the OFF, was investigated in four different localities and cultivars. Olive fruit fly infestations caused a general reduction of the fungal diversity, a higher quantity of the total DNA and an increase in taxa that remained unidentified or had unknown roles. The infestations led to imbalanced fungal communities with the growth of taxa that are usually outcompeted. While it was difficult to establish a cause-effect link between fly infestation and specific fungi, it is clear that the fly alters the natural microbial balance, especially the low abundant taxa. On the other hand, the most abundant ones, were not significantly influenced by the insect. In fact, despite the slight variation between the sampling locations, Aureobasidium, Cladosporium, and Alternaria, were the dominant genera, suggesting the existence of a typical olive fungal microbiome.
|
|
| 4. |
- Abdelfattah, Ahmed, et al.
(författare)
-
Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies
- 2018
-
Ingår i: Biological control (Print). - : ACADEMIC PRESS INC ELSEVIER SCIENCE. - 1049-9644 .- 1090-2112. ; 120
-
Tidskriftsartikel (refereegranskat)abstract
- Microorganisms are the main drivers shaping the functioning and equilibrium of all ecosystems, contributing to nutrient cycling, primary production, litter decomposition, and multi-trophic interactions. Knowledge about the microbial assemblies in specific ecological niches is integral to understanding the assemblages interact and function the function, and becomes essential when the microbiota intersects with human activities, such as protecting crops against pests and diseases. Metabarcoding has proven to be a valuable tool and has been widely used for characterizing the microbial diversity of different environments and has been utilized in many research endeavors. Here we summarize the current status of metabarcoding technologies, the advantages and challenges in utilizing this technique, and how this pioneer approach is being applied to studying plant diseases and pests, with a focus on plant protection and biological control. Current and future developments in this technology will foster a more comprehensive understanding of microbial ecology, and the development of new, innovative pest control strategies.
|
|
| 5. |
- Abdelfattah, Ahmed, et al.
(författare)
-
Revealing Cues for Fungal Interplay in the Plant-Air Interface in Vineyards
- 2019
-
Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 10
-
Tidskriftsartikel (refereegranskat)abstract
- Plant-associated microorganisms play a crucial role in plant health and productivity. Belowground microbial diversity is widely reported as a major factor in determining the composition of the plant microbiome. In contrast, much less is known about the role of the atmosphere in relation to the plant microbiome. The current study examined the hypothesis that the atmospheric microbiome influences the composition of fungal communities of the aboveground organs flowers, fruit, and leaves) of table grape and vice versa. The atmosphere surrounding grape plantings exhibited a significantly higher level of fungal diversity relative to the nearby plant organs and shared a higher number of phylotypes 5,536 OTUs, 40.3%) with the plant than between organs of the same plant. Using a Bayesian source tracking approach, plant organs were determined to be the major source of the atmospheric fungal community 92%). In contrast, airborne microbiota had only a minor contribution to the grape microbiome, representing the source of 15, 4, and 35% of the fungal communities of leaves, flowers, and fruits, respectively. Moreover, data indicate that plant organs and the surrounding atmosphere shared a fraction of each other's fungal communities, and this shared pool of fungal taxa serves as a two-way reservoir of microorganisms. Microbial association analysis highlighted more positive than negative interactions between fungal phylotypes. Positive interactions were more common within the same environment, while negative interactions appeared to occur more frequently between different environments, i. e., atmosphere, leaf, flower, and fruit. The current study revealed the interplay between the fungal communities of the grape phyllosphere with the surrounding air. Plants were identified as a major source of recruitment for the atmospheric microbiome, while the surrounding atmosphere contributed only a small fraction of the plant fungal community. The results of the study suggested that the plant-air interface modulates the plant recruitment of atmospheric fungi, taking a step forward in understanding the plant holobiont assembly and how the atmosphere surrounding plants plays a role in this process. The impact of plants on the atmospheric microbiota has several biological and epidemiological implications for plants and humans.
|
|
| 6. |
- Belgacem, Imen, et al.
(författare)
-
Transcriptomic Analysis of Orange Fruit Treated with Pomegranate Peel Extract (PGE)
- 2019
-
Ingår i: PLANTS. - : MDPI AG. - 2223-7747. ; 8:4
-
Tidskriftsartikel (refereegranskat)abstract
- A Pomegranate Peel Extract (PGE) has been proposed as a natural antifungal substance with a wide range of activity against plant diseases. Previous studies showed that the extract has a direct antimicrobial activity and can elicit resistance responses in plant host tissues. In the present study, the transcriptomic response of orange fruit toward PGE treatments was evaluated. RNA-seq analyses, conducted on wounded fruits 0, 6, and 24 h after PGE applications, showed a significantly different transcriptome in treated oranges as compared to control samples. The majority (273) of the deferentially expressed genes (DEGs) were highly up-regulated compared to only 8 genes that were down-regulated. Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis showed the involvement of 1233 gene ontology (GO) terms and 35 KEGG metabolic pathways. Among these, important defense pathways were induced and antibiotic biosynthesis was the most enriched one. These findings may explain the underlying preventive and curative activity of PGE against plant diseases.
|
|
| 7. |
- Malacrinò, Antonino, et al.
(författare)
-
A Metabarcoding Survey on the Fungal Microbiota Associated to the Olive Fruit Fly
- 2017
-
Ingår i: Microbial Ecology. - : SPRINGER. - 0095-3628 .- 1432-184X. ; 73:3, s. 677-684
-
Tidskriftsartikel (refereegranskat)abstract
- The occurrence of interaction between insects and fungi is interesting from an ecological point of view, particularly when these interactions involve insect pests and plant pathogens within an agroecosystem. In this study, we aimed to perform an accurate analysis on the fungal microbiota associated to Bactrocera oleae (Rossi) through a metabarcoding approach based on 454 pyrosequencing. From this analysis, we retrieved 43,549 reads that clustered into 128 operational taxonomic units (OTUs), of which 29 resulted in the “core” associate fungi of B. oleae. This fungal communitywasmainly represented by sooty mould fungi, such as Cladosporium spp., Alternaria spp. and Aureobasidium spp., by plant pathogens like Colletotrichum spp. and Pseudocercospora spp., along with several other less abundant taxa whose ecology is unclear in most of the cases. Our findings lead to new insights into the microbial ecology of this specific ecological niche, enabling the understanding of a complex network of interactions within the olive agroecosystem.
|
|
| 8. |
- Malacrinó, Antonino, et al.
(författare)
-
Fungal communities associated with bark and ambrosia beetles trapped at international harbours
- 2017
-
Ingår i: Fungal ecology. - : Elsevier. - 1754-5048 .- 1878-0083. ; 28, s. 44-52
-
Tidskriftsartikel (refereegranskat)abstract
- Bark and ambrosia beetles (Coleoptera; Scolytinae) establish trophic relationships with fungi, which could be also agents of plant diseases. Orthotomicus erosus (Wollaston) and Xyleborinus saxesenii (Ratzeburg) are two species of Palaearctic origin that have been introduced in several countries around the world. Here, we investigated their associated fungal communities using individuals trapped at harbours in their native range, without strictly focusing on nutritional symbionts. Targeting the ITS2 region of the fungal rDNA through pyrosequencing, we retrieved taxa known to be agents of plant diseases, taxa never previously reported associated with these beetle species, and sequence clusters not linked to any known fungus. These findings underline that surveillance at harbours should be extended to the fungi associated with trapped bark and ambrosia beetles, taking into account their role as potential vectors of plant pathogens. (C) 2017 Elsevier Ltd and British Mycological Society. All rights reserved.
|
|
| 9. |
- Malacrinò, Antonino, et al.
(författare)
-
Molecular analysis of the fungal microbiome associated with the olive fruit fly Bactrocera oleae
- 2015
-
Ingår i: Fungal ecology. - : ELSEVIER SCI LTD. - 1754-5048 .- 1878-0083. ; 18, s. 67-74
-
Tidskriftsartikel (refereegranskat)abstract
- A molecular approach was used to investigate the fungal microbiome associated with Bactrocera oleae a major key pest of Olea europea, using the ITS2 region of the ribosomal DNA (rDNA) as barcode gene. Amplicons were cloned and a representative number of sequenced fragments were used as barcode genes for the identification of fungi. The analysis of the detected sequence types (STs) enabled the identification of a total of 34 phylotypes which were associated with 10 fungal species, 3 species complexes and 8 genera. Three phylotypes remained unresolved within the order Saccharomycetales and the phylum Ascomycota because of the lack of closely related sequences in GenBank. Cladosporium was the most abundantly detected genus, followed by Alternaria and Aureobasidium, well-known components of olive sooty moulds. Interestingly, Colletotrichum sp. and other fungal plant pathogens were also detected, leading to potential new insights into heir epidemiology. (C) 2015 Elsevier Ltd and The British Mycological Society. All rights reserved.
|
|
| 10. |
- Piombo, Edoardo, et al.
(författare)
-
Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens
- 2021
-
Ingår i: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:1
-
Forskningsöversikt (refereegranskat)abstract
- Globalization has a dramatic effect on the trade and movement of seeds, fruits and vegetables, with a corresponding increase in economic losses caused by the introduction of transboundary plant pathogens. Current diagnostic techniques provide a useful and precise tool to enact surveillance protocols regarding specific organisms, but this approach is strictly targeted, while metabarcoding and shotgun metagenomics could be used to simultaneously detect all known pathogens and potentially new ones. This review aims to present the current status of high-throughput sequencing (HTS) diagnostics of fungal and bacterial plant pathogens, discuss the challenges that need to be addressed, and provide direction for the development of methods for the detection of a restricted number of related taxa (specific surveillance) or all of the microorganisms present in a sample (general surveillance). HTS techniques, particularly metabarcoding, could be useful for the surveillance of soilborne, seedborne and airborne pathogens, as well as for identifying new pathogens and determining the origin of outbreaks. Metabarcoding and shotgun metagenomics still suffer from low precision, but this issue can be limited by carefully choosing primers and bioinformatic algorithms. Advances in bioinformatics will greatly accelerate the use of metagenomics to address critical aspects related to the detection and surveillance of plant pathogens in plant material and foodstuffs.
|
|
