Impact of Cultivation and Origin on the Fruit Microbiome of Apples and Blueberries and Implications for the Exposome

Abstract

Vegetables and fruits are a crucial part of the planetary health diet, directly affecting human health and the gut microbiome. The objective of our study was to understand the variability of the fruit (apple and blueberry) microbiome in the frame of the exposome concept. The study covered two fruit-bearing woody species, apple and blueberry, two countries of origin (Austria and Finland), and two fruit production methods (naturally grown and horticultural). Microbial abundance, diversity, and community structures were significantly different for apples and blueberries and strongly influenced by the growing system (naturally grown or horticultural) and country of origin (Austria or Finland). Our results indicated that bacterial communities are more responsive towards these factors than fungal communities. We found that fruits grown in the wild and within home gardens generally carry a higher microbial diversity, while commercial horticulture homogenized the microbiome independent of the country of origin. This can be explained by horticultural management, including pesticide use and post-harvest treatments. Specific taxonomic indicators were identified for each group, i.e., for horticultural apples: Pseudomonas, Ralstonia, and Stenotrophomonas. Interestingly, Ralstonia was also found to be enriched in horticultural blueberries in comparison to such that were home and wildly grown. Our study showed that the origin of fruits can strongly influence the diversity and composition of their microbiome, which means that we are exposed to different microorganisms by eating fruits from different origins. Thus, the fruit microbiome needs to be considered an important but relatively unexplored external exposomic factor.

Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonisation of Listeria monocytogenes

“…Sphingomonas aerolata, one of the most abundant members of the resident microbiota of this factory, was significantly more prevalent in the production area of the facility. S. aerolata is a psychrotolerant bacteria firstly isolated from the air of a building [73] and to our knowledge, this is the first time that has been detected in food processing environments, although it has been detected by 16S rRNA amplicon sequencing in fruits [77]. Other taxa, mainly within the Pseudomonas genus, showed higher abundance in the preparation area, although these species represented a minor proportion of the whole community (<0.125%).…”

Investigating the inoculum dynamics of Cladosporium on the surface of raspberry fruits and in the air

“…Larger scale distances on farms may facilitate greater climatic and vegetational differences that impact bacteria more than fungi, with fungi potentially being more evenly present due to their airborne spore movement. Geographical location significantly affects the microbiome of multiple fruit crops (Abdelfattah et al, 2021; Mezzasalma et al, 2018; Wicaksono et al, 2023). Therefore, future research on raspberry microbiomes may benefit from including more than one geographical location to understand how large an impact it has on the microbiome composition compared to other factors.…”

“…Cladosporium infections are suspected to occur more frequently in warm and humid environments (O'Neill et al, 2012), such as those conditions within polythene tunnels. Cladosporium is also frequently reported as being prevalent in plant tissues as an endophyte (Franco Ortega et al, 2020; Wicaksono et al, 2023), with the relative abundance being 37.8% in one study in homogenized strawberries (Abdelfattah et al, 2016). It is currently unknown, however, how dominant Cladosporium is within the epiphytic microbiome of fruit, where disease development likely begins for skin lesions.…”

The edible plant microbiome: evidence for the occurrence of fruit and vegetable bacteria in the human gut

“…As suggested previously, due to human activities, r-strategic microbes will become more prevalent while K-strategists will continue to gradually disappear. 43 Examples reflecting the impact of global agriculture on fruit microbiomes were mentioned by Wassermann et al, 44 identifying a storage-specific resistome in exported apples, and by Wicaksono et al, 45 showing the impact of cultivation on the apple and blueberry microbiota and enrichment of r-strategic microbes. On the other hand, our study provides the basis to develop joint solutions for plant and human health by application of probiotics as recently proposed.…”