The Fungal and Bacterial Rhizosphere Microbiome Associated With Grapevine Rootstock Genotypes in Mature and Young Vineyards

Abstract

The microbiota colonizing the rhizosphere and the endorhizosphere contribute to plant growth, productivity, carbon sequestration, and phytoremediation. Several studies suggested that different plants types and even genotypes of the same plant species harbor partially different microbiomes. Here, 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. Linear discriminant analysis identified specific bacterial (i.e., Bacillus ) and fungal (i.e., Glomus ) taxa associated with grapevine rootstocks. Host genotype did not predict any summary metrics of rhizosphere α- and β-diversity in the young vineyard. Regarding black-foot associated pathogens, a significant correlation between sequencing reads and qPCR was observed. In conclusion, grapevine rootstock genotypes in the mature vineyard were associated with different rhizosphere microbiomes. The latter could also have been affected by age of the vineyard, soil properties or field management practices. 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.

Fungal Endophytic Community Associated with Guarana (Paullinia cupana Var. Sorbilis): Diversity Driver by Genotypes in the Centre of Origin

“…The present results suggest that structuring of guarana fungal community (cultivable organisms) is directed both by the genetics of the host plant as well as by the geographic location, especially in leaves. These results are in line with previous studies of grapevines [ 99 ] and tomato [ 100 ] plants that have shown that different plant organs, genotypes of the same plant species and even sampling positions in the farmland can harbor partially different microbiomes. Guarana had high dominance of Colletotrichum and Fusarium , known as well established organisms, with different life style types [ 98 ].…”

Saline and Arid Soils: Impact on Bacteria, Plants, and Their Interaction

“…Basic soils such as desert generally have higher relative abundance of Actinobacteria than Acidobacteria [ 188 ]. This observation is confirmed by the study on the vineyards of Berlanas [ 189 ]: the vineyards have a more acidic soil than the desert, and the Acidobacteria (13.7% and 16.4%) immediately follow the Proteobacteria and the Actinobacteria (almost 50% of the total).…”

Grapevine pruning time affects natural wound colonization by wood-invading fungi

“…samples (Berlanas et al, 2019). If precise indication of aerial spore load for one specific fungal 543 species is required, quantitative PCR would become the tool of choice.…”