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

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.

Microbial Diversity of Reconstituted, Degraded, and Agricultural Soils Assessed by 16S rDNA Multi-Amplicon Sequencing

“…As regards details from the core vs. specific/unique microbiome analysis, at phylum level two bacterial phyla, Latescibacterota and NB1-j, were uniquely present in AS samples, although at low frequencies (both <1%). Those phyla are reported to be present in several environments although their function is still unknown (Jimenez et al, 2020;Dries et al, 2021;Hamdan et al, 2008;Coelho et al, 2016). At order level Chtonomonadales, a bacterial order capable to utilize different carbohydrate substrates as carbon and energy sources (Wang (Baureder and Hederstedt, 2013), and Bacteroidales, a bacterial order present in human and animal faeces (Levantesi et al, 2012), were encountered almost only in DS samples, although not in a dominant fashion.…”

The Grapevine Microbiome to the Rescue: Implications for the Biocontrol of Trunk Diseases

“…Proteobacteria is a very large and diverse phylum that includes bacteria with a broad variety of metabolic capabilities; Alpha-, Beta-, Gamma- and Delta-Proteobacteria are the classes mostly described in soil studies. However, Dries and colleagues only detected Alpha- and Gamma-Proteobacteria and in their study [ 34 ]. Both classes are considered copiotrophs (r-strategist), which are able to easily colonize environments characterized by an abundance of nutrients, such as the rhizosphere [ 58 ].…”

“…Moreover, rootstocks are important in preventing problems due to soil conditions, such as salinity or poor mineral nutrition [ 56 ]. It is therefore not surprising that considerable effort has been made in recent years to determine how grapevine rootstock genotypes shape the rhizosphere microbiome [ 23 , 29 , 31 , 34 ].…”

“…More recently, Dries and colleagues [ 34 ] analyzed the bacterial microbiome associated with different grapevine rootstocks ( Table 1 ). At the phylum level, the rhizosphere was dominated by Acidobacteriota (35%), Proteobacteria (22%), Latescibacteriota (15%), Methylomirabilota (6%) and Gemmatimonadota (4%).…”

Screening of epiphytic rhizosphere-associated bacteria in Argentinian Malbec and Cabernet-Sauvignon vineyards for potential use as biological fertilisers and pathogen-control agents

“…The combination of different sustainable agricultural methods for the production of crops has involved researching and applying new technologies, which study the adequate use of bacterial isolates and identifying their PGP traits, relying on their efficiency to survive and thrive under laboratory conditions as well as in field cultivation experiments (Souza et al, 2015). The favourable response to soil or plant inoculation with PGPR varies considerably depending on the bacteria employed, the plant and soil type and the environmental conditions (Dries et al, 2021;Fedele et al, 2020;Santoyo et al, 2021). These aspects imply that the biogeographical origin and environmental conditions constitute relevant considerations in the search for new bacterial isolates.…”