Assessing the impact of plant genetic diversity in shaping the microbial community structure of Vitis vinifera phyllosphere in the Mediterranean

Abstract

The aerial surface of the plant (phyllosphere) is the habitat of complex microbial communities and the structure of this microbiome may be dependent on plant genetic factors, local environment or interactions between them. In this study, we explored the microbial diversity present in the phyllosphere of a very diverse set of grapevine cultivars representing the three genetic pools of the species, grown on an experimental plot at Montpellier (French Mediterranean region). We assessed microbiome variation in the phyllosphere using amplicon sequencing of the 16S rRNA gene and of the internal transcribed spacer (ITS), according to the grapevine genetic pools or cultivars, and organs (i.e. leaves and grape berries). The observed microbiome was complex; out of 542 bacterial genera; Pseudomonas, Pantoea, Sphingomonas, and Acinetobacter were the most abundant and almost ubiquitously present across the samples, and out of 267 fungal genera; Aureobasidium, Alternaria, Mycosphaerella and Aspergillus were most represented. Our results illustrated that the microbial taxa were almost uniformly distributed among the genetic pools and only a few cultivar or genetic pool level differences were found, but a very clear differential taxa abundance was found between the leaf and berry samples. Some genus level associations were also observed with certain genetic pools.

Seasonal epiphytic microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments

“…In contrast to the bacterial communities, the fungal communities were mainly affected by the sampling period, during which PD and evenness showed similar trends for both the biocontrol and Cu-treated leaves. This is in line with Singh et al 31 who showed that the shift of the microbial community in samples collected at different times was detected for fungi only. The fact that phylogenetic diversity increased, together with evenness, until December suggested that the complexity of the fungal community increased due to a higher number of similarly abundant taxa.…”

“…This allowed the conclusion to be drawn that the different amount detected in relative abundance for the Lactobacillaceae family was due to the presence of reads belonging to MW-1. Finally the bacterial community, which appeared to be relatively stable throughout the season, reflected the composition already reported by 31 and 35 . The dominance of Proteobacteria and Firmicutes highlighted in their paper, was consistent with the phyla-distribution shown in the present study.…”

“…Understanding the structure and dynamics of microbial communities in the phyllosphere is important because of their effects on plant protection and plant growth. Since the structure and dynamics of the microbiome are affected by environmental factors such as geography 30 , grape cultivar 31 and climate 32 , this study focused on different treatments applied in two blocks of the same vineyard. Both treatments, Cu and MW-1, were applied to control fungal diseases.…”

“…Sample preparation and DNA extraction. The tubes containing the leaves were thawed at room temperature and 20 ml of a washing solution was subsequently added (Singh et al 31 ) and placed on a rocket inverter, applying one hour of shaking rotation. After this, the leaves were discarded using sterile pincettes.…”

Endophytic fungi of olive tree and their exploitation in the biological control of olive anthracnose = Hongos endofíticos del olivo y su aprovechamiento para el control biológico de la antracnosis del olivo

“…However, we are yet to know what forces determine specific fungal community assemblages (Compant et al, 2016), in particular in woody perennials. Endophytic fungal surveys conducted in woody perennials over the last years showed that plant organ is a significant factor in shaping endophytic fungal assemblage Abdelfattah et al, 2015;Singh et al, 2017;Singh et al, 2018;Ren et al, 2019). In general, the main plant tissues that have been analysed in these studies were vegetative organs, such as leaves, twigs, barks, stems and roots Abdelfattah et al, 2015;Singh et al, 2017;Singh et al, 2018;Ren et al, 2019), and only a few studies have looked for fungal endophytes in reproductive organs (e.g., flowers or fruits) (Abdelfattah et al, 2015;Singh et al, 2018;Ren et al, 2019).…”