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

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PubMed ID: 31178845

Imagen Publicación

Berlanas C, Berbegal M, Elena G, Laidani M, Cibriain JF, Sagües A, Gramaje D

Front Microbiol. 2019. doi: 10.3389/fmicb.2019.01142

COMMENT: Common grapevine (Vitis vinifera L.) is one of the most economically important fruit crop worldwide. This study characterized the rhizosphere microbial community composition across five commercial grapevine rootstock genotypes at two vineyards usign High-Throughput Amplicon Sequencing. Understanding of the bacterial and fungal microbiota in the rhizosphere and the interactions between microbiota and grapevine will facilitate the development of new strategies for grapevine protection.

Objective

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 (HTAS)....In addition, we used quantitative Polymerase Chain Reaction (qPCR) approach to measure the relative abundance and dynamic changes of fungal pathogens associated with black-foot disease, one of the main soil-borne fungal diseases affecting grapevine production worldwide.

Main results

Grapevine rhizosphere samples of five rootstocks were collected at two vineyards located in Aldeanueva de Ebro (“Aldea”) (La Rioja, Spain) and Olite (Navarre, Spain).

Bacterial communities of rhizosphere soil samples did not differ significantly between vineyards... However, α-diversity differed among sites when studying the fungal microbiota, and principal coordinates analysis (PCoA) of Bray Curtis data demonstrated that vineyard was the primary source of β-diversity.

Comparing the fungal and bacterial microbiota of the two vineyards, 82.9 and 58.7% of bacterial and fungal OTUs, respectively, were shared between vineyards, demonstrating the existence of a “core” grape phylogeny that is independent of the growing region

In both vineyards, the bacterial phyla Proteobacteria (26.1 and 28.1% in Aldea and Olite, respectively) and Actinobacteria (24.1 and 18.5%) represented almost 50% of the total bacteria detected......Regarding the fungal taxa, the most abundant fungal phylum was Ascomycota (66.6 and 69.9% in Aldea and Olite, respectively), followed by Basidiomycota (20.1 and 11.5%) and Zygomycota (8.9 and 15.2%)...

Bacterial and fungal diversity in rhizosphere soil samples differed significantly among rootstocks in Aldea vineyard.

Host genotype was the most important factor in structuring bacterial (R2 = 0.65, P < 0.001) and fungal (R2 = 0.86, P < 0.001) communities in the entire dataset, and also when the data were split by year and date

Our results demonstrate that bacterial microbiome varied profoundly between years. This pattern was consistent to community-level measure of α- diversity in both Aldea and Olite vineyards...Regarding the fungal microbiome, richness also varied between vineyards and increased between 2016 and 2017 in both vineyard

DNA of Cylindrocarpon-like asexual morphs was detected in all rootstock rhizosphere samples, in both vineyards and years,..The year and vineyard factors had a significant effect on Cylindrocarpon-like asexual morphs DNA concentration detected (P < 0.01).....The analysis showed a positive significant correlation between the number of OTUs and the Cylindrocarpon-like asexual morphs DNA quantified using the real-time approach (P < 0.01, Spearman correlation coefficient = 0.72)

Conclusion

We have studied the effects of genotype, year, sampling date, and location on bacterial and fungal communities in the grapevine rhizosphere. We found that grapevine genotype was the most important factor in shaping the microbiome in the mature vineyard. Many bacterial and fungal species were found in all rootstocks and in both locations in our study, demonstrating the existence of a “core” grape phylogeny that is independent of the growing region.

Contributor

Diana López-Farfán