The microbiota colonizing the rhizosphere and the endorhizosphere contribute to plant growth, productivity, carbon sequestration, and phytoremediation. We characterize the rhizosphere bacterial and fungal microbiota across five grapevine rootstock genotypes cultivated in the same soil at two vineyards and sampling dates over 2 years by 16S rRNA gene and ITS high-throughput amplicon sequencing. In addition, we use quantitative PCR (qPCR) approach to measure the relative abundance and dynamic changes of fungal pathogens associated with black-foot disease. The objectives were to (1) unravel the effects of rootstock genotype on microbial communities in the rhizosphere of grapevine and (2) to compare the relative abundances of sequence reads and DNA amount of black-foot disease pathogens. Host genetic control of the microbiome was evident in the rhizosphere of the mature vineyard. Microbiome composition also shifted as year of sampling, and fungal diversity varied with sampling moments. Regarding black-foot associated pathogens, a significant correlation between sequencing reads and qPCR was observed. A more comprehensive study is needed to decipher the cause of the rootstock microbiome selection and the mechanisms by which grapevines are able to shape their associated microbial community. Understanding the vast diversity of bacteria and fungi in the rhizosphere and the interactions between microbiota and grapevine will facilitate the development of future strategies for grapevine protection.
Berlanas, C., Berbegal, M., Elena, G., Laidani, M., Cibriain, J.F., Sagües, A., and Gramaje, D. 2019. The fungal and bacterial rhizosphere microbiome associated with grapevine rootstock genotypes in mature and young vineyards. Frontiers in Microbiology 10:1142.