Abstract
ABSTRACTThe 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.
Highlights
Vitis vinifera, is the main grape species grown for fruit and wine production over the world
As a first step towards this goal, we explored the bacterial and fungal diversity in the phyllosphere of leaf and berry samples from a set of rather diverse grapevine cultivars that belongs to the three genetic pools of the cultivated grapevine (Nicolas et al 2016), in the French Mediterranean region
Our analysis based on high throughput 16S and internal transcribed spacer (ITS) profiling identifies the presence of complex microbiota in the phyllosphere of leaves and fruits of grapevine cultivars grown in our Mediterranean vineyard and it is dominated by bacterial genera of Pseudomonas, Sphingomonas, Enterobacter and the fungal genera of Aureobasidium, Alternaria, Cladosporium, respectively which is concordant with the findings of other grapevine related studies (Zarraonaindia et al 2015; Zhang et al 2017)
Summary
Vitis vinifera (subsp. vinifera L.), is the main grape species grown for fruit and wine production over the world. Vinifera L.), is the main grape species grown for fruit and wine production over the world It is a natural host of a wide variety of prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects (Schulz et al 1999). The phyllosphere (in general) harbors complex microbial communities involved in many crucial functions such as nitrogen fixation (Jones 1970), carbon sequestration (Bringel and Couée 2015), degradation of pesticides and organic pollutants (Brandl et al 2001; Kishore et al.2005; Bulgarelli et al 2013) It is a significant and ubiquitous habitat for microorganisms and an open system that microbes can invade by migration from the atmosphere, soil, other plants and insects (Lugtenberg et al 2002; Williams et al 2013). Microbial populations on phyllosphere are known to live and thrive under harsh environmental factors such as UV radiation, air pollution, temperature fluctuations, water and nutrient availability (Andrews and Harris. 2000; Lugtenberg et al 2002; Müller and Ruppel 2014)
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