Understanding grapevine-microbiome interactions: implications for viticulture industry

Iratxe Zarraonaindia; Jack A Gilbert

doi:10.15698/mic2015.05.204

Understanding grapevine-microbiome interactions: implications for viticulture industry

Microb Cell. 2015 May 4;2(5):171-173. doi: 10.15698/mic2015.05.204.

Authors

Iratxe Zarraonaindia¹, Jack A Gilbert²

Affiliations

¹ Argonne National Laboratory, Institute for Genomic and Systems Biology, Argonne, Illinois, USA. ; Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa (Bizkaia), Spain.
² Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA. ; Department of Surgery, University of Chicago, Chicago, Illinois, USA. ; Marine Biological Laboratory, Woods Hole, Massachusetts, USA. ; College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.

Abstract

Until recently, the analysis of complex communities such as that of the grapevine-microbe holobiont has been limited by the fact that most microbes are not culturable under laboratory conditions (less than 1%). However, metagenomics, the study of the genetic material recovered directly from environmental samples without the need for enrichment or of culturing, has led to open an unprecedented era in the field of microbiology. Importantly, this technological advance has now become so pervasive that it is being regularly applied to explore soils and plants of agricultural interest. Interestingly, many large companies are taking notice, with significant financial investment being used to exploring ways to manipulate the productivity, disease resistance and stress tolerance for crops by influencing the microbiome. To understand which microbes one needs to manipulate to influence this valuable characteristics, we need to sequence the microbiome and capture the genetic and hence functional metabolic information contained therein. For viticulture and other agricultural fields where the crop is also associated to particular flavor properties that may also be manipulated, understanding how the bacteria, fungi and viruses influence the development and hence chemical makeup of the crop is essential.

Keywords: Merlot microbiome holobiont; Terroir; biotechnological applications.

Publication types

Comment

Grants and funding

This work was supported by the Earth Microbiome Project, the FMC Center for Agricultural and Environmental Biotechnology, and a postdoctoral research grant (DKR program) to I.Z. from the Education, Universities and Investigation Department of the Basque government. This work was supported in part by the U.S Department of Energy under contract DE-AC02-06CH11357 and was completed with resources provided by the University of Chicago Research Computing Center. We are grateful to Gilles Martin for giving us access to the Long Island vineyards in this study and assisting with the sampling and to Guilherme Martins from USC Oenologie-INRA/Bordeaux Science Agro for collecting and extracting the DNA of the Merlot samples from Château Camensac (Bordeaux). We acknowledge Sarah O’Brien and Timothy Vugteveen (Argonne National Laboratory) for their involvement in the soil chemistry analysis, as well as Sean M. Gibbons for his assistance with QIIME analysis.