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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 #325029
Title: Metagenomic analysis of fungal diversity on strawberry plants and the effect of management practices on the fungal community structure of aerial organs

Author
item ABDELFATTAH, AHMED - University Of Reggio Calabria
item Wisniewski, Michael
item NICOSA, MARIA - University Of Reggio Calabria
item CACCIOLA, SANTA - University Of Reggio Calabria
item SCHENA, LEONARDO - University Of Reggio Calabria

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/20/2016
Publication Date: 8/4/2016
Citation: Abdelfattah, A., Wisniewski, M.E., Nicosa, M., Cacciola, S.O., Schena, L. 2016. Metagenomic analysis of fungal diversity on strawberry plants and the effect of management practices on the fungal community structure of aerial organs. PLoS One. DOI: 10.1371/journal.pone.0160470.

Interpretive Summary: Strawberry (Fragaria x ananassa) is an important horticultural crop worldwide that is produced both conventionally and organically in open fields, greenhouses, and in plastic covered tunnels. Strawberries are susceptible to several fungal pathogens and thus, require the use of fungicide treatments to prevent economic losses. Although previous studies of the strawberry fungal or bacterial community have been previously reported, these studies were based on the use of techniques where the organisms need to be cultured on petri plates in order to be defined and so the results did not represent the full complement of organisms present, nor did it represent the full spectrum of individual aerial plant parts, e.g. leaves, fruits, and flowers. Furthermore, these studies did not investigate the impact of conventional chemical treatments of fungal populations. In the present study, Next Generation Sequencing (NGS) was used to broadly identify all organisms present on different aerial organs of strawberry plants grown under plastic covers and determine the impact of fungicide applications on the diversity of the fungal community. The technique relies on the ability to just extract total DNA from the plant surface and use gene-specific primers to amplify gene sequences that can be used to identify the presence of an organism. Therefore, there is no need to rely on culturing any organisms. Results indicated that a broad diversity of organisms exist on the surface of strawberry plants, many more species than previously identified by culturing techniques. A one-month interruption of applying fungicides also had a significant effect on the composition of the fungal community. The high abundance (70-99%) of just two genera may be a direct consequence of the use of an intensive chemical pesticide schedule used on the farm that was sampled. The differences observed between treated and untreated (no chemical treatments for one month) strawberries indicate that natural fungal communities are very resilient and that the composition and species abundance in these communities can quickly change in response to modified environmental conditions. The information obtained in this study will be used as a baseline to determine the effect of various cultural and biological practices on fungal and bacterial diversity of fruit crops.

Technical Abstract: Metabarcoding, defined as Next Generation Sequencing (NGS) of amplicons of the ITS2 region (DNA barcode), was used to identify the composition of the fungal community on different strawberry organs i.e. leaves, flowers, and immature and mature fruits grown on a farm using disease and insect control practices that entailed the routine use of various chemical pesticides. Strawberry plants supported a high diversity of microbial organisms, although two genera, Botrytis and Cladosporium, were more highly abundant than all the other identified genera, representing 70-99% of the relative abundance (RA) of all detected sequences. Leaves supported the most diverse fungal community, followed by flowers. Some of the detected taxa are known to be resident on strawberries. On the other hand, several plant pathogens of other plant species that would not be intuitively expected to be present on strawberry plants were detected, while some common strawberry pathogens were less evident or not detected. The study also indicated a high degree of diversity in the ITS sequence within certain taxonomic groups. The interruption of chemical treatments for one month resulted in a significant modification in the structure of the fungal community and the RA of specific genera. The overwhelming abundance of just two fungal genera may be a consequence of the intensive chemical pesticide schedule commonly utilized in the investigated farm. The differences observed between treated samples and samples untreated for a month indicate, however, that natural fungal communities exhibit a great plasticity whose composition can quickly change in response to modified environmental conditions.