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47th World Congress on Microbiology

London, UK

Elisa Bona

Elisa Bona

Università del Piemonte Orientale, Italy .

Title: Vitis vinifera rhizosphere microbiome: metagenomic and metaproteomic approaches


Biography: Elisa Bona


Title: Vitis vinifera rhizosphere microbiome: metagenomic and metaproteomic approaches
              E. Bona1, P. Cesaro1, G. Novello1, L. Boatti 1,2, V. Magnelli1, N. Massa1, V. Todeschini1, M. Manfredi 1,3, G. Lingua1, F. Mignone 1,2, E. Marengo 1,3, G. Berta1, E. Gamalero1

1 Università del Piemonte Orientale, DiSIT, Alessandria, Vercelli, Italy

2 SmartSeq s.r.l., spin-off of the Università del Piemonte Orientale, Alessandria, Italy

3 Isalit srl, spin-off of the Università del Piemonte Orientale, Novara, Italy


Vitis vinifera is a Mediterranean crop with relevant impact on the Italian landscape, culture and economy. The rhizosphere is a hotspot where the release of root exudates modulates bacterial density and diversity. Despite the high bacterial number found in rhizosphere, only 1-10% of the soil bacteria are able to grow on laboratory media, so that the majority of the bacterial cells in soil results to be viable, unculturable, but active; even more, this percentage change according to the host plant. Thanks to culture-independent methods (metagenomics) the complexity of the soil/rhizosphere microbial community has been explored. However, metagenomics doesn’t provide information regarding the activity and the molecular interactions between the bacterial communities and roots. Proteins are the drivers of cellular activities encoded by the genome. Therefore, proteomic tools could be useful to gain information about microbial community activity and to better understand the real interactions pathways between roots and soil. A comparison between the microbial community structure in rhizosphere and bulk soil using metagenomics (pyrosequencing of 16S rDNA) and proteomics (MS/MS analysis of the total protein occurring in soil samples) was performed.

Actinobacteria were the dominant class in all the soil samples, followed by Proteobacteria, Gemmatimonadetes and Bacteroidetes. While Actinobacteria and Proteobacteria are well known as dominant in soil, for the first time, members belonging to Gemmatimonadetes have been observed in vineyard soils.  Bacteria belonging to Streptomyces, Bacillus, Bradyrhizobium, Burkholderia and Pseudomonas genera were the most active. Concerning the biological activity of these genera, in the rhizosphere, we observed the exclusive presence of phosphorus metabolic process and the regulation of: biosynthetic, cellular, macromolecule, nitrogen compound and primary metabolic process.

Our results underlined the difference between the metagenomic and metaproteomic approaches and the potentiality of proteomics in describing the environmental bacterial communities and their activity.