However, an evident HDAC activity assay distinction between the leaf-derived profiles and those from the stems could be observed in DGGE, as it was observed for the total bacteria, Alphaproteobacteria and Betaproteobacteria. Two groups were formed at 54% in the resulting dendrogram based on the location in the plant (Figure 3). Plants from the genotype LSID003 seemed to select the fungal community present in their leaves, as a separate group was formed in the dendrogram at

approximately 20%. Different bands were retrieved from the gel (marked in Figure 3 with the letter F, followed by a number), and their phylogenetic comparison revealed 29 sequences associated with the genus Lasiodiplodia (F2-F4, F6, F8-F10, F12, F13, F15-F18, C188-9 F20, F21, F23-F26, F30-F35,

F47, F50, F52, F53), 11 with Botryosphaeria (F1, F5, F7, F11, F14, F19, F22, F36, F48, F49, F51), seven with Mycosphaerella (F38-F40, F42, F43, F45, F46), two with Corynespora (F55, F56) and one with each of the following genera: Neoaleurodiscus (F27), Ceratobasidium (F29), Heteroacanthella (F37), Pantospora (F41), Passalora (F44) and Massarinaceae (F54). While bands related to the genera Neoaleurodiscus and Heteroacanthella were found in the stems, Mycosphaerella, Pantospora, Passalora, Massarinaceae and Corynespora were exclusively detected in the leaves. Although a few members of the Basidiomycota (Ceratobasidium and Heteroacanthella) were present, the majority of the bands from both leaves and stems were associated Selleckchem PARP inhibitor with the Ascomycota. Principal

component analysis (PCA) of DGGE patterns Ordination of the PCR-DGGE profiles using PCA supported the aforementioned effects of plant location on the bacterial (Alphaproteobacteria and Betaproteobacteria) and fungal communities (Figure 6a, b, c, d, f). This effect was not clearly observed for the actinobacterial community (Figure 6e). Figure 6 Principal component analysis (PCA) ordination diagram with stem and leaf samples from Lippia sidoides genotypes LSID003, LSID006, LSID104 and LSID105 and the components of the essential oil (thymol and carvacrol) as variables not (arrows): first axis – horizontal, second axis – vertical. The fraction of the total variance accounted for by each axis is indicated in parentheses. The corresponding communities analyzed are as follows: (a) (b) total bacteria, (c) Alphaproteobacteria, (d) Betaproteobacteria, (e) Actinobacteria and (f) fungi. The genotypes are represented by the three first numbers (LSID – 003, 006, 104 and 105), followed by C or F for stem and leaf samples and T1 and T2 corresponding to the replicates. The first PCA axes explained 51.2, 32.8, 25.0, 26.3, 25.9 and 23.4% of the variance, whereas the second ones covered 20.1, 23.6, 19.2, 20.4, 14.6 and 14.7% (Figure 6a, b, c, d, e, f, respectively). With respect to the total bacterial communities, PCA ordination of the samples showed a tendency for these communities to group based on their origin, i.e.