| 1. |
- Abdelfattah, Ahmed, et al.
(författare)
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Effect of Washing, Waxing and Low-Temperature Storage on the Postharvest Microbiome of Apple
- 2020
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Ingår i: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:6
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Tidskriftsartikel (refereegranskat)abstract
- There is growing recognition of the role that the microbiome plays in the health and physiology of many plant species. However, considerably less research has been conducted on the postharvest microbiome of produce and the impact that postharvest processing may have on its composition. Here, amplicon sequencing was used to study the effect of washing, waxing, and low-temperature storage at 2 degrees C for six months on the bacterial and fungal communities of apple calyx-end, stem-end, and peel tissues. The results of the present work reveal that tissue-type is the main factor defining fungal and bacterial diversity and community composition on apple fruit. Both postharvest treatments and low temperature storage had a strong impact on the fungal and bacterial diversity and community composition of these tissue types. Distinct spatial and temporal changes in the composition and diversity of the microbiota were observed in response to various postharvest management practices. The greatest impact was attributed to sanitation practices with major differences among unwashed, washed and washed-waxed apples. The magnitude of the differences, however, was tissue-specific, with the greatest impact occurring on peel tissues. Temporally, the largest shift occurred during the first two months of low-temperature storage, although fungi were more affected by storage time than bacteria. In general, fungi and bacteria were impacted equally by sanitation practices, especially the epiphytic microflora of peel tissues. This research provides a foundation for understanding the impact of postharvest management practices on the microbiome of apple and its potential subsequent effects on postharvest disease management and food safety.
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| 2. |
- Abdelfattah, Ahmed, et al.
(författare)
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Evidence for host-microbiome co-evolution in apple
- 2022
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 234:6, s. 2088-2100
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Tidskriftsartikel (refereegranskat)abstract
- Plants evolved in association with a diverse community of microorganisms. The effect of plant phylogeny and domestication on host–microbiome co-evolutionary dynamics are poorly understood.Here we examined the effect of domestication and plant lineage on the composition of the endophytic microbiome of 11 Malus species, representing three major groups: domesticated apple (M. domestica), wild apple progenitors, and wild Malus species.The endophytic community of M. domestica and its wild progenitors showed higher microbial diversity and abundance than wild Malus species. Heirloom and modern cultivars harbored a distinct community composition, though the difference was not significant. A community-wide Bayesian model revealed that the endophytic microbiome of domesticated apple is an admixture of its wild progenitors, with clear evidence for microbiome introgression, especially for the bacterial community. We observed a significant correlation between the evolutionary distance of Malus species and their microbiome.This study supports co-evolution between Malus species and their microbiome during domestication. This finding has major implications for future breeding programs and our understanding of the evolution of plants and their microbiomes.
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| 3. |
- Abdelfattah, Ahmed, et al.
(författare)
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Global analysis of the apple fruit microbiome : are all apples the same?
- 2021
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 23:10, s. 6038-6055
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Tidskriftsartikel (refereegranskat)abstract
- We present the first worldwide study on the apple (Malus x domestica) fruit microbiome that examines questions regarding the composition and the assembly of microbial communities on and in apple fruit. Results revealed that the composition and structure of the fungal and bacterial communities associated with apple fruit vary and are highly dependent on geographical location. The study also confirmed that the spatial variation in the fungal and bacterial composition of different fruit tissues exists at a global level. Fungal diversity varied significantly in fruit harvested in different geographical locations and suggests a potential link between location and the type and rate of postharvest diseases that develop in each country. The global core microbiome of apple fruit was represented by several beneficial microbial taxa and accounted for a large fraction of the fruit microbial community. The study provides foundational information about the apple fruit microbiome that can be utilized for the development of novel approaches for the management of fruit quality and safety, as well as for reducing losses due to the establishment and proliferation of postharvest pathogens. It also lays the groundwork for studying the complex microbial interactions that occur on apple fruit surfaces.
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| 4. |
- Castoria, Raffaello, et al.
(författare)
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Biological Control of Mycotoxigenic Fungi in Fruits
- 2008
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Ingår i: Mycotoxins in Fruits and Vegetables" (R. Barkai-Golan and N. Paster, eds.). - San Diego : Elsevier. - 9780123741264 ; , s. 311-333
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Mycotoxins are toxic metabolites produced by fungi. The ability to produce mycotoxins is found in some fungal pathogens of plants and/or molding agents of food and feed, and has a noteworthy repercussion on the quality and safety of food products. Mycotoxin contaminations now present one of the most insidious challenges to overcome in food safety. Their importance is evident by the constant attention paid at them internationally, because of their harmful impact on animal and human health as well as on the economy. The most prevalent toxigenic fungi on fresh fruits belong to the genera Aspergillus, Penicillium and Alternaria, which pose serious mycotoxicological risks essentially in postharvest and processed food products. Although the ability of these fungi to produce and contaminate fresh and processed fruit with mycotoxins is well established, mostly they are referred to in the pathological context as rot-causing pathogens. In this regard, there is a need to discuss not only postharvest losses attributed to these pathogens, but also the toxic metabolites they produce. The use of microbial antagonists for the control of postharvest pathogens, including mycotoxigenic fungi, will be discussed in detail, taking into account the commercial potential and perspectives of the practical application of these biological control agents and their mechanisms of action. Also the pathogenicity factors of postharvest pathogens and the possible role of mycotoxins are presented, with regard to their possible influence on and interaction with the biocontrol agents. Other approaches for the control of postharvest pathogens such as physical (e.g., controlled atmosphere, heat treatment) and chemical control are presented in separate chapters of this book. Their integration with microbial antagonists should also be taken into account. In this chapter, however, integration of biocontrol agents with chemical control only is discussed, while combination of these beneficial microorganisms with controlled atmospheres is still in its infancy.
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| 5. |
- Castoria, Raffaello, et al.
(författare)
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Biological Control of Mycotoxigenic Fungi in Fruits
- 2008
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Ingår i: Mycotoxins in Fruits and Vegetables. - : Elsevier. - 9780123741264 ; , s. 311-333
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Mycotoxins are toxic metabolites produced by fungi. The ability to produce mycotoxins is found in some fungal pathogens of plants and molding agents of food and feed, and has a noteworthy repercussion on the quality and safety of food products. Mycotoxin contaminations present one of the most insidious challenges to meet in food safety. Their importance is evident in the constant attention paid to them internationally, because of their harmful impact on animal and human health as well as on the economy. The most prevalent toxigenic fungi on fresh fruits belong to the genera Aspergillus, Penicillium, and Alternaria, which pose serious mycotoxicological risks essentially in postharvest and processed food products. The use of microbial antagonists for the control of postharvest pathogens, including mycotoxigenic fungi, is briefly explained in this chapter taking into account the commercial potential and perspectives of the practical application of these biological control agents and their mechanisms of action.
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| 6. |
- Piombo, Edoardo, et al.
(författare)
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Characterizing the Fungal Microbiome in Date (Phoenix dactylifera) Fruit Pulp and Peel from Early Development to Harvest
- 2020
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Ingår i: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:5
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Tidskriftsartikel (refereegranskat)abstract
- Date palm (Phoenix dactylifera) is considered to be a highly important food crop in several African and Middle Eastern countries due to its nutritional value and health-promoting properties. Microbial contamination of dates has been of concern to consumers, but very few works have analyzed in detail the microbial load of the different parts of date fruit. In the present work, we characterized the fungal communities of date fruit using a metagenomic approach, analyzing the data for differences between microbial populations residing in the pulp and peel of Medjool dates at the different stages of fruit development. The results revealed that Penicillium, Cladosporium, Aspergillus, and Alternaria were the most abundant genera in both parts of the fruit, however, the distribution of taxa among the time points and tissue types (peel vs. pulp) was very diverse. Penicillium was more abundant in the pulp at the green developmental stage (Kimri), while Aspergillus was more frequent in the peel at the brown developmental stage (Tamer). The highest abundance of Alternaria was detected at the earliest sampled stage of fruit development (Hababauk stage). Cladosporium had a high level of abundance in peel tissues at the Hababauk and yellow (Khalal) stages. Regarding the yeast community, the abundance of Candida remained stable up until the Khalal stage, but exhibited a dramatic increase in abundance at the Tamer stage in peel tissues, while the level of Metschnikowia, a genus containing several species with postharvest biocontrol activity, exhibited no significant differences between the two tissue types or stages of fruit development. This work constitutes a comprehensive metagenomic analysis of the fungal microbiome of date fruits, and has identified changes in the composition of the fungal microbiome in peel and pulp tissues at the different stages of fruit development. Notably, this study has also characterized the endophytic fungal microbiome present in pulp tissues of dates.
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| 7. |
- Piombo, Edoardo, et al.
(författare)
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Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens
- 2021
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Ingår i: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:1
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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.
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| 8. |
- Solanki, Manoj Kumar, et al.
(författare)
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Shifts in the Composition of the Microbiota of Stored Wheat Grains in Response to Fumigation
- 2019
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- While the wheat-associated microbiome is of major agricultural importance, little is known about the alterations in wheat grain microbial community composition during storage. Characterization of the bacterial and fungal communities in stored wheat grains revealed the impact of phosphine fumigation, one of the most effective methods to eliminate insects in stored commodities, on the composition of the wheat grain microbiome. High-throughput amplicon sequencing of the bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) region was used to analyze the wheat grain microbiome at different times over as 6 months period of storage. Higher bacterial diversity was found across the samples during the first (immediately after harvest) and second (3 months later) time points, with a predominance of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes. A two-fold decrease in the number of bacterial operational taxonomic units (OTUs) was observed in wheat grains at the last time point (6 months later), following phosphine treatment. In contrast to the effect of phosphine on bacteria, it did not affect fungal diversity in stored grains. The majority of fungal sequences were assigned to Ascomycota, followed by Basidiomycota, Glomeromycota, and unidentified fungi, which were evenly distributed throughout the storage period. Alpha and beta diversity analyses were confirmed by examination of the cultured microbial taxa obtained from the stored wheat grains. Mycotoxin analysis of wheat grains collected after phosphine fumigation revealed the presence of Fusarium toxins, primarily deoxynivalenol (DON). Several mycotoxigenic Fusarium spp. were also detected in the same samples. Results of the present study indicate that microbiome of stored, whole wheat grains was strongly affected by phosphine fumigation, which changed the structure of the microbial community leading to shifts in species composition toward mycotoxigenic strains. A better understanding of the complex interactions within the microbial communities of stored grains will assist in the development of novel biocontrol strategies to overcome mycotoxin contamination.
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