Using next generation sequencing to describe epiphytic microbiota associated with organic and conventionally managed apples
Abstract
Its seems likely that agricultural management as diverse as certified organic and conventional IPM practices would impact the microbiota associated with crop surfaces differently. We sampled organic and conventionally managed apples at multiple time -points in a growing season and characterized the bacterial taxa associated with replicates of each treatment type. Surprisingly, no evidence of significant differences persisting across multiple time -points was observed. Significant differential abundance of certain taxa was documented but when it was, it was primarily associated with a single time-point making it difficult to understand if these observations resulted from an environmental or a treatment effect. Principal component analyses demonstrated that sampling time -point explained more of the differences between bacterial communities than treatment. Description of dominant shared bacterial families for both organic and conventional samples included Oxalobacteraceae, Pseudomonadaceae, Sphingomonadaceae and Enterobacteriaceae.
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Introduction
Organic agriculture is part of efforts to streamline agricultural practices to provide safer and more sustainably harvested foods. “Organic” became a certified practice with the passage of the Organic Food Production Act in the 1990 Farm Bill. For certified organic practices, the use of synthetic pesticides, genetically modified organisms, sewage sludges, irradiation, and other practices deemed to be detrimental to society and the environment are prohibited. While produce labeled ‘‘organic’’ means that a set of prescribed practices has been followed - these practices vary enormously by crop and geographic region.
To understand what “organic” means for 5 different fruits and vegetables at any supermarket would involve extensive study of each commodity, where it was grown, weather pressures during the growing season, and what the regulations and approved materials may be for organic certification in each specific region. Questions persist regarding how organic management may contrast with conventional management in terms of impact on harvest, plant pathology, and food safety. To better understand how organic and conventional management impacted an apple crop with regard to bacterial microbiota found on surfaces of fruits and leaves, we designed the experiment presented here. The microbial ecology associated with the surfaces of fruits and leaves is significant for all aforementioned considerations. For food safety, it is important to assess whether or not, a greater risk of exposure to human pathogens may correlate with organically or conventionally managed foods. Organic agriculture often relies on fertilizers or pesticides that are more natural materials - thus often supporting a more robust “native” microbial ecology that could be transferred to the crop. Fertilizers in particular host a wealth of bacterial and fungal species that may directly impact the safety of the crop especially if there is direct contact with edible surfaces of plants.
Here, we examine the impact of organic and conventional management on apples (cultivar Enterprise) grown in Queenstown, Maryland. Because so many different materials are used in the two management types (Table 1), we hypothesized that the organic and conventional fertilization and pesticide schedules would impact the epiphytic microbiota of the apple crop differently. Apple trees were grown in a randomized block design with five replicates of each apple tree under both certified organic and conventional IPM (integrated pest management) management. Trees were planted in 2003, with the first certified organic crop harvested in 2006. All samples for the work presented here were collected in 2008, after three consecutive years of certified organic and conventional management.
Conclusion
Despite the drastically different agricultural inputs that were applied to the organically and conventionally managed trees, very few statistically significant difference s were observed between samples from the two treatments and those that were, were associated with a single time -point, making it difficult to discern if it was a treatment effect, a temporal effect or an environmental effect. The high level of shared bacterial and fungal taxa suggests that environmental parameters (such as wind, dust, or air) may have had an equally strong influence on the epiphytic microbiota as the organic and conventional management did.