Abstract
Apples are among the most consumed fruits world-wide. They represent a source of direct human exposure to bacterial communities, which is less studied. We analyzed the apple microbiome to detect differences between tissues and the impact of organic and conventional management by a combined approach of 16S rRNA gene amplicon analysis and qPCR, and visualization using fluorescence in situ hybridization and confocal laser scanning microscopy (FISH-CLSM). Each apple fruit harbors different tissues (stem, peel, fruit pulp, seeds, and calyx), which were colonized by distinct bacterial communities. Interestingly, fruit pulp and seeds were bacterial hot spots, while the peel was less colonized. In all, approximately 108 16S rRNA bacterial gene copy numbers were determined in each g apple. Abundances were not influenced by the management practice but we found a strong reduction in bacterial diversity and evenness in conventionally managed apples. In addition, despite the similar structure in general dominated by Proteobacteria (80%), Bacteroidetes (9%), Actinobacteria (5%), and Firmicutes (3%), significant shifts of almost 40% of bacterial genera and orders were monitored. Among them, especially bacterial signatures known for health-affecting potential were found to be enhanced in conventionally managed apples. Our results suggest that we consume about 100 million bacterial cells with one apple. Although this amount was the same, the bacterial composition was significantly different in conventionally and organically produced apples.
Highlights
The host-associated microbiota is involved in health issues of the host; this was shown for humans and plants as well (Derrien and van Hylckama Vlieg, 2015; Berg et al, 2017)
Gene copy numbers of bacterial 16S rRNA per gram tissue of organic and conventional apples were measured by Quantitative PCR (qPCR) inquiry (Figure 1)
Bacterial abundances were observed to be mostly consistent between the management analogs of each tissue; no significant differences (p < 0.05) were observed according to non-parametric Kruskal–Wallis/False Discovery Rate (FDR)
Summary
The host-associated microbiota is involved in health issues of the host; this was shown for humans and plants as well (Derrien and van Hylckama Vlieg, 2015; Berg et al, 2017). Despite being composed and partly deeply embedded within the host, microbial communities are essentially open and interconnected ecosystems (Berg, 2015). This connection and the exchange between microbiomes are less understood, despite their importance to health reflected in the one health concept (Flandroy et al, 2018). It was shown that plant-associated microbiota including bacteria, fungi and viruses transiently colonized the gut (David et al, 2014); forming our transient microbiome (Derrien and van Hylckama Vlieg, 2015). More knowledge on fresh produce-associated microbiota and a holistic view on the system is crucial for food safety inquiries (Blau et al, 2018)
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