Rootstocks Shape Their Microbiome-Bacterial Communities in the Rhizosphere of Different Grapevine Rootstocks.

Leonie Dries,Simone Bussotti,Robert Kunz,Otmar Löhnertz,Anne Vortkamp,Carlo Pozzi,Sylvia Schnell

doi:10.3390/microorganisms9040822

Abstract

The microbiota associated with the rhizosphere is responsible for crucial processes. Understanding how the plant and its bacterial community interact is of great importance to face the upcoming agricultural and viticultural challenges. The composition of the bacterial communities associated with the rhizosphere of grapevines is the result of the interaction between many drivers: biogeography, edaphic factors, soil management and plant genotype. The experimental design of this study aimed to reduce the variability resulting from all factors except the genotype of the rootstock. This was made possible by investigating four ungrafted grapevine rootstock varieties of the same age, grown on the same soil under the same climatic conditions and managed identically. The bacterial communities associated with the rhizosphere of the rootstocks 1103 Paulsen, 140 Ruggeri, 161-49 Couderc and Kober 5BB were characterized with the amplicon based sequencing technique, targeting regions V4–V5 of 16S rRNA gene. Linear discriminant analysis effect Size (LEfSe) analysis was performed to determine differential abundant taxa. The four rootstocks showed similarities concerning the structure of the bacteria assemblage (richness and evenness). Nonetheless, differences were detected in the composition of the bacterial communities. Indeed, all investigated rootstocks recruited communities with distinguishable traits, thus confirming the role of rootstock genotype as driver of the bacteria composition.

Highlights

The continuous improvement of cultivation-independent techniques is driving a paradigm shift in the field of biology; the expression of a specific phenotype is no longer determined solely by the interaction between genotype and environment but has to take into account the host-associated microorganisms [1]
The experimental design of this study aimed to reduce the variability resulting from environmental factors to unravel the effect of the genotype of the grapevine rootstock on the bacterial communities in the rhizosphere
According to Berlanas et al [14], the dominant phyla found in two vineyards located in Northeastern Spain were Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes

Summary

Introduction

The continuous improvement of cultivation-independent techniques is driving a paradigm shift in the field of biology; the expression of a specific phenotype is no longer determined solely by the interaction between genotype and environment but has to take into account the host-associated microorganisms (microbiota) [1]. The microbiome (the genome of the microbiota) provides adaptability and metabolic diversity, broadening the plant capacity to overcome environmental changes and to cope with challenging conditions [2,3]. The distribution of the microbiota is not even throughout the plant, which can be interpreted as an assembly of several niches. Agricultural productivity is based on microbial activity, much of which occurs in the soil [5].

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Conclusion