# Does Organic Farming Increase Raspberry Quality, Aroma and Beneficial Bacterial Biodiversity?
## 3 Results  
### Characterization of Raspberry Culture Dependent and Independent Bacteriome  
The composition of bacterial communities of raspberry fruit cultivated with organic or IPM strategies were assessed by NGS analysis of 16S rRNA gene. Sufficient sequencing effort was assessed (Figure S1). Community composition at the phylum level differed according to the cultivation method. Although both organic and IPM fruits were dominated by Bacilli and Alpha-proteobacteria, these phyla represented respectively 33% and 20% of total operational taxonomic units (OTUs) in IPM fruit, and 76 and 15% of total OTUs in organic fruits (Figure 1). Moreover, IPM fruits showed a higher bacterial biodiversity than organic ones (Shannon Index, H\({}^{\prime}\) = 3.6 and 2, respectively) and also higher taxa evenness (J\({}^{\prime}\) = 0.64 and 0.4, respectively; Table S1). The bacteriocin of organic fruit was dominated by _Glucobacter_ spp. (73%), whereas IPM raspberries were colonized by several different taxa (_Brevbacillus_ 14%, _Methylobacterium_ 4%) (Figure 1). _Glucobacter_ spp. were absent in IPM fruits. To visualize differences among the bacterial microbiomes of the two cultivation methods, PCA was performed according to bacterial families (Figure 2a). Organic produced fruit had more even composition of the bacterial community with berries discriminated only by PC2 (13% of the total variance). Despite the high uniformity of organic fruit, the analysis also highlighted that the differences in bacterial families between berries produced with organic and IPM practices provided only a partial discrimination of berries. Acetobacteraceae and Enterobacteriaceae were the first two families presenting the highest loading values for PC1 (85% of the expected variance) and thus mainly responsible for fruit discrimination (Figure 2b). The total culturable bacterial population, expressed in log (colony-forming units (CFU)/fruit g), was higher in organic (6.1 \(\pm\) 0.7) than IPM (5.6 \(\pm\) 0.1). The analysis of culturable bacterial population indicated that IPM and organic fruit differentiated by few genera. _Rosenbergiella_ was present only in IPM fruit, whereas _Tatumella_, _Klebsiella_ and _Cronobacter_ genera were found only in organic one (Table 1). IPM and organic unique bacterial isolates were screened for their in vitro plant growth promoting activities (Table 2). Figure 1: Krona chart showing bacterial community composition at phylum, order, class, family and genus level for (**a**) integrated pest management (IPM) and (**b**) organic raspberry fruits ‘Enrosadira’. Indole-3-acetic-acid (IAA) producing bacteria, namely _Pantoea agglomerans_ str. 2 and _Tatumella terrea_, were isolated only in organic fruit, whereas the sole acetoin-producing bacterium, _Enterobacter_ spp. str. 2, was found on IPM fruit. All the isolates from organic fruit, but only one from IPM fruit, could release ammonia. Concerning siderophore production, _Klebsiella oxytocin_ and _Enterobacter_ spp. (str. 1 and 2) were the only species accreting this activity in organic and IPM fruit, respectively. Finally, none of the isolated strains neither in organic, nor IPM berries presented an ACC deaminase activity.