Grapevine Microbiomics: Bacterial Diversity on Grape Leaves and Berries Revealed by High-Throughput Sequence Analysis of 16s Rrna Amplicons

Abstract

We used the culture-independent method of high-throughput pyrosequencing of 16S ribosomal RNA (rRNA) gene amplicons to analyze the diversity of bacteria associated with the leaf and berry surfaces of 'Chardonnay' grape in a vineyard close to harvest. Combined, more than half of all bacterial sequences were classified as Proteobacteria. Other well-represented phyla were the Firmicutes, Bacteroidetes, and Actinobacteria. The most abundantly represented genera were Sphingomonas, Hymenobacter, Bacillus, Pseudomonas, Skermanella, Leuconostoc, Massilia, Methylobacterium, Cellvibrio, and Curtobacterium. Together, these top 10 genera accounted for almost one-third of all sequences. We observed differences in the composition of bacterial communities between leaves and berries. Members of the genera Sphingomonas, Hymenobacter and Methylobacterium were abundant on foliage, whereas Achromobacter, Flavobacterium and Cellvibrio were typical for the fruit. Moreover, certain Pseudomonas species appeared to associate exclusively with leaf surfaces, while others were found more frequently on berries. Unanticipated was the discovery of a novel Proteobacterium that dominated the bacterial community on berry surfaces. Our results form the basis for future investigations into the relationship between the structure of microbial communities on grape leaves and berries and the ecosystem (dis)services that these communities provide to grape growers at different pre-and post-harvest stages of production.

Resilience of the Natural Phyllosphere Microbiota of the Grapevine to Chemical and Biological Pesticides

“…Ascomycota and Basidiomycota were the most abundant fungal phyla, and a substantial part of sequenced reads was assigned to unannotated fungal OTU, which possibly represent environmental sequences of uncultured fungi. The dominant bacterial genera were Sphingomonas, Frigoribacterium, Pseudomonas, and Curtobacterium, as previously reported for grapevine leaves (23,24,63). Sphingomonas and Pseudomonas are widespread on plant leaves (64,65), while Curtobacterium are commonly found in soil, and they possibly spread by aerial migration (24).…”

“…However, the impact of commercial fungicides and/or promising biocontrol agents on the phyllosphere microbiota has not yet been investigated in grapevine. Phyllosphere communities of the grapevine have been analyzed mainly in terms of bacterial composition in relation to populations of the rhizosphere, bark, and berries (23,24). The objective of the present study was to investigate the effect of a chemical fungicide based on sterol biosynthesis inhibition (penconazole) and a biocontrol agent, Lysobacter capsici AZ78 (AZ78), on the taxonomic structure and functional properties of indigenous microbial communities on grapevine leaves at three different locations.…”

Microbial terroir for wine grapes

“…The well-known influence of bacteria and fungi in the wine fermentation, particularly lactic acid bacteria and yeasts, has led to the development of commercial products, including specific fungal taxa to improve wine fermentation processes and flavor. However, the role of prokaryotes was considered to be limited to the malolactic fermentation processes, or even to be only detrimental to fermentation (6). However, metagenomic studies are revealing that grapes can harbor a more diverse microbial community than previously anticipated, for example in botrytized wine ferments (7).…”

“…Therefore, as well as soil-derived microbial colonization through root endophytes, there are additional routes for colonization, including soil dust contamination by rain splash, or from people during harvesting, or other agricultural practices; indeed, even the phyllosphere (leaf zone) of nearby plants may transfer microbial taxa through aerial or insect transportation, which suggests even the local biodiversity may impact which taxa are found in which regions (6). Although it is expected that climatic factors could constrain the biogeographic distribution of grape microbiome, the soil characteristics (e.g., availability of nutrients for the plant) and soil structure still has a great impact on constraining the microbiota that could colonize the remaining plant niches (11)(12)(13)(14).…”

Microbiomics: An Approach to Community Microbiology

“…Microbial compositions of the phylloplane provide insight into protecting the plants from various diseases and insects and help in improving plant health. Leveau and Tech ( 2011 ) studied the leaf and fruit surfaces of grapes using 16S rRNA gene sequencing. They used eight leaves and two berries as samples and extracted the microbial DNA from their surfaces.…”