Plant growth promotion potential is equally represented in diverse grapevine root-associated bacterial communities from different biopedoclimatic environments

Abstract

Plant-associated bacteria provide important services to host plants. Environmental factors such as cultivar type and pedoclimatic conditions contribute to shape their diversity. However, whether these environmental factors may influence the plant growth promoting (PGP) potential of the root-associated bacteria is not widely understood. To address this issue, the diversity and PGP potential of the bacterial assemblage associated with the grapevine root system of different cultivars in three Mediterranean environments along a macrotransect identifying an aridity gradient were assessed by culture-dependent and independent approaches. According to 16S rRNA gene PCR-DGGE, the structure of endosphere and rhizosphere bacterial communities was highly diverse (P = 0.03) and was associated with a cultivar/latitudinal/climatic effect. Despite being diverse, the bacterial communities associated with Egyptian grapevines shared a higher similarity with the Tunisian grapevines than those cultivated in North Italy. A similar distribution, according to the cultivar/latitude/aridity gradients, was observed for the cultivable bacteria. Many isolates (23%) presented in vitro multiple stress resistance capabilities and PGP activities, the most frequent being auxin synthesis (82%), insoluble phosphate solubilisation (61%), and ammonia production (70%). The comparable numbers and types of potential PGP traits among the three different environmental settings indicate a strong functional homeostasis of beneficial bacteria associated with grape root.

Figure 1

DGGE analysis of grapevine root-associated microbial communities. (a) Representative DGGE gels of the separation of 16S rRNA gene fragments along a denaturing gradient. The analyzed fractions were root tissues (E), rhizosphere (R), root-surrounding soil (S), and bulk soil (B) of three replicate plants of grapevine from a vineyard in Italy (left panel), Tunisia (central panel), and Egypt (right panel). (b) Principal component analysis (PCA) of the plot line profiles that were obtained from DGGE fingerprinting of the bacterial community. E replicates are represented by a circle, R samples by a triangle, S samples by a rhombus, and B by a square. (c)-(d) ANOVA analysis was performed on the average values of the line plot score along axis 1 and 2, respectively, of PCA analysis in order to assess the degree of similarities among plant and soil-associated bacterial communities in the three study sites. Different letters (a and b), shown at the top of the scatter plots in the graph, indicate a statistical significance at P ≤ 0.05 according to ANOVA analysis.

Figure 2

Comparison of the structure of endosphere and rhizosphere bacterial communities associated with grapevines along an aridity transect in the Mediterranean basin. (a) Principal component analysis (PCA) of the PCR-DGGE profiles of endophyte (E) and rhizosphere (R) fractions associated with grapevine cultivated in Italy (IT), Tunisia (TN), and Egypt (ET). Samples were run and analyzed in triplicate. (b)-(c) Statistical analysis was applied to the average values of endophyte and rhizosphere samples along axis 1 and axis 2, respectively, of the PCA analysis. Statistical significance (P) was evaluated according to the Student's t-test and is indicated in every graph.

Figure 3

Phylogenetic identification of DNA fragments that were excised from the DGGE gel and successfully amplified and sequenced.

Figure 4

Phylogenetic identification of culturable bacteria associated with grapevine plant and soil fractions. (a)-(b) Bacteria repartition in endosphere (ROOT), rhizosphere (RHIZ), root-surrounding soil (SSR), and bulk soil (BULK) of grapevine grown in Italy (IT), Tunisia (TN), and Egypt (ET) according to the class and genus level, respectively.

Figure 5

PGP potential of grapevine-associated bacteria. (a)–(c) Percentage of isolates showing an increasing number of PGP abilities in the strain collection isolated from grapevine grown in vineyards located in Italy, Tunisia, and Egypt, respectively. (d)–(f) Percentage of isolates displaying the assayed PGP traits and abiotic stress tolerance in the bacterial collection of strains associated with grapevine cultivated in Italy, Tunisia, and Egypt, respectively.