Impact of Organic and Conventional Management on the Phyllosphere Microbial Ecology of an Apple Crop

Abstract

Bacterial communities associated with the phyllosphere of apple trees (Malus domestica cv. Enterprise) grown under organic and conventional management were assessed to determine if increased biological food safety risks might be linked with the bacterial communities associated with either treatment. Libraries of 16S rRNA genes were generated from phyllosphere DNA extracted from a wash made from the surfaces of leaves and apples from replicated organic and conventional treatments. 16S rRNA gene libraries were analyzed with software designed to identify statistically significant differences between bacterial communities as well as shared and unique phylotypes. The identified diversity spanned eight bacterial phyla and 14 classes in the pooled organic and conventional libraries. Significant differences between organic and conventional communities were observed at four of six time points (P < 0.05). Despite the identification of significantly diverse microfloras associated with organic and conventional treatments, no detectable differences in the presence of potential enteric pathogens could be associated with either organic or conventional management. Neither of the bacterial genera most commonly associated with produce-related illness outbreaks (Salmonella and Escherichia) was observed in any of the libraries. The impressive bacterial diversity that was documented in this study provides a valuable contribution to our developing understanding of the total microbial ecology associated with the preharvest phyllospheres of food crops. The fact that organic and conventional phyllosphere bacterial communities were significantly different at numerous time points suggests that crop management methods may influence the bacterial consortia associated with the surfaces of fruits and vegetables.

Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables

“…We found the surface bacterial communities of spinach, lettuce, and tomatoes to be numerically dominated by Gammaproteobacteria, a pattern which has also been noted in previous studies [5], [15], [16], [37], [38]. Similarly, Ottesen et al [18] observed that Alphaproteobacteria was the most abundant bacterial class on apples, and we found the family Sphingomonadaceae within the class Alphaproteobacteria was the most abundant family present on apples. It is more difficult to directly compare our results with the large body of research on produce-associated bacteria that has been conducted using culture-based techniques as such techniques do not typically quantify proportions of bacteria belonging to specific taxonomic groups, rather binning them into operationally-defined groups determined by the culturing media used.…”

“…From this previous work, a few key patterns emerge: (1) Different produce types and cultivars can harbor different abundances of specific bacterial groups [9], (2) farming and storage conditions may influence the composition and abundances of microbial communities found on produce [3], [5], [15]–[18], and (3) non-pathogenic microbes may interact with and inhibit microbial pathogens found on produce surfaces [7], [9], [19]–[21]. Despite this body of work, we still have a limited understanding of the diversity of produce-associated microbial communities, the factors that influence the composition of these communities, and the distributions of individual taxa across produce types (particularly those taxa that are difficult to culture).…”

“…Consumers in developed nations are commonly exposed to differences in farming practices through their choice between organic and conventionally farmed produce items. Organic farming practices can differ from conventional farming practices in a variety of ways, including the types of fertilizer and pesticides that are used, and these differences have the potential to impact microbial community structure on produce surfaces [4], [17], [18], [26]. However, we do not know if these potential effects of farming practices on produce-associated microbial communities are evident across a wide range of produce types and whether such effects persist up until the point that produce is purchased and consumed.…”

Bacterial community diversity and variation in spray water sources and the tomato fruit surface

“…Similar results were obtained when the fruit surface communities living on apple trees under conventional and organic management were compared, where only low abundance groups differed between the two environments [17]. Similarly, no effect on the levels of fecal and total coliforms was observed when reclaimed water with higher coliform counts, and well water were sprayed on six horticultural crops [14].…”

The science, development, and commercialization of postharvest biocontrol products

“…As a result, very little is known about the overall diversity and composition of microbial communities on harvested produce and how these communities vary across produce types. Based on recent studies on this topic (Rudi et al, 2002;Ponce et al, 2008;Ottesen et al, 2009;Rastogi et al, 2012;Leff and Fierer, 2013;), a few key patterns are emerging: (1) different produce types and cultivars can harbor different levels (abundances) of specific microbial groups (Critzer and Doyle, 2010), (2) farming and storage conditions can influence the composition and abundances of microbial communities found on produce, and (3) non-pathogenic microbes can interact with and inhibit microbial pathogens found on produce surfaces (Shi et al, 2009;Critzer and Doyle, 2010;Teplitski et al, 2011). Despite this recent body of work, we still have a limited understanding of the diversity of produce-associated microbial communities, their function, the factors that influence the composition of these communities after harvest and during storage, and the distribution of individual taxa (particularly those taxa that are difficult to culture) across different commodities.…”