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ARS Home » Northeast Area » Kearneysville, West Virginia » Appalachian Fruit Research Laboratory » Innovative Fruit Production, Improvement, and Protection » Research » Publications at this Location » Publication #333599
Title: Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase

Author
item ABDELFATTAH, AHMED - University Of Reggio Calabria
item Wisniewski, Michael
item DROBY, SAMIR - Volcani Center (ARO)
item SCHENA, LEONARDO - University Of Reggio Calabria

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/12/2016
Publication Date: 11/1/2016
Citation: Abdelfattah, A., Wisniewski, M.E., Droby, S., Schena, L. 2016. Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase. Horticulture Research. DOI: 10.1038/hortres.2016.47.

Interpretive Summary: Fruits serve as hosts to many microorganisms that colonize the surface (epiphytes) or live within (endophytes) their tissues. Several of these fungi are known to be phytopathogenic and responsible for significant economic losses, before and after harvest, while other resident microorganisms are considered beneficial and can influence the severity of disease symptoms by directly interacting with pathogens or by inducing resistance in the host. Microbial studies, however, have been mainly based on the isolation and culturing of microorganisms which can often be problematic. Thus, our current understanding of the fruit microbiome is largely based on the ability to isolate, culture, and identify the most abundant microorganisms which are estimated to represent only a small fraction of the total estimated microbial diversity. Therefore, a metagenomics approach based on the sequencing of highly-conserved DNA sequences was used to assess the fungal diversity of organic and conventional 'Red Delicious' apple fruit. The objective of the study was to investigate: 1) the composition fungal communities in different fruit parts, including stem end, calyx end, peel, and wounded flesh ("location" effect); 2) changes in the composition of fungal communities in the above fruit parts over a two-week period of storage at room temperature ("time" effect); and 3) the potential impact of management practices (organic vs. conventional) on apple fungal communities ("practices" effect). The results indicated that unique communities of fungi occupied different portions of the apple (stem end vs. calyx end vs. peel tissues vs. wounded tissue). Little changes occurred in the composition of the fungal community over a two-week period of storage at room temperature. Apple fruits exhibited a highly complex and diverse assemblage of fungal species that never would have been detected by culturing techniques. Some differences were observed between 'organic' and 'conventional' fruit, but these differences were difficult to attribute to management practices since the study was conducted on store-bought apples and thus, many uncontrolled elements may have also contributed to the observed differences. This study lays the foundation for more detailed studies on the role of the microbiota on fruit quality, shelf life, and nutrition.

Technical Abstract: The fungal diversity in harvested apples from organic or conventional management practices was analyzed in different fruit locations (stem end, calyx end, peel, and wounded flesh) shortly after fruit purchase (T1) and after two weeks of storage (T5). A total of 5,760,162 high quality fungal sequences were recovered and assigned to 8,504 OTUs. Members of the phylum Ascomycota were dominant in all samples and accounted for 91.6% of the total number of detected sequences. This was followed by Basidiomycota (8%), Chytridiomycota (0.1%), and unidentified fungi (0.3%). Alpha and beta diversity analyses revealed the presence of significantly different fungal populations in the investigated fruit parts. Among detected fungi, the genus Penicillium prevailed in the peel and in the wounded flesh, while Alternaria spp. prevailed in the calyx and stem end samples which included apple core tissues. Several taxonomic units that appear to be closely-related to fungi associated with human secondary infections were present in peel and wounds, but their presence was relatively rare with very low abundancy. Moreover, significantly different populations were revealed in organic and conventional apples, and this result was consistent in all investigated fruit parts (CE, PE, SE, and WF). Several unique taxa were exclusively detected in organic apples suggesting that management practices may have been a contributing factor in determining the taxa present; however, other factors such as differential handling or processing of the fruit and that were not controlled in the present study may have also contributed to the observed differences. In contrast, little differences were revealed in the two assessment times (T1 and T5). Results of the present study represent an advancement of the current knowledge on the fungal microbiome in the harvested fruit tissues.