Effect of Site and Phenological Status on the Potato Bacterial Rhizomicrobiota

Abstract

The potato is the fourth major food crop in the world. Its cultivation can encounter problems, resulting in poor growth and reduced yield. Plant microbiota has shown an ability to increase growth and resistance. However, in the development of effective microbiota manipulation strategies, it is essential to know the effect of environmental variables on microbiota composition and function. Here, we aimed to identify the differential impact of the site of cultivation and plant growth stage on potato rhizosphere microbiota. We performed a 16S rRNA gene amplicon sequencing analysis of rhizospheric soil collected from potato plants grown at four sites in central Italy during two phenological stages. Rhizomicrobiota was mainly composed of members of phyla Acidobacteriota, Actinobacteriota, Chloroflexi, and Proteobacteria and was affected by both the site of cultivation and the plant stages. However, cultivation sites overcome the effect of plant phenological stages. The PiCRUST analysis suggested a high abundance of functions related to the biosynthesis of the siderophore enterobactin. The presence of site-specific taxa and functional profiling of the microbiota could be further exploited in long-term studies to evaluate the possibility of developing biomarkers for traceability of the products and to exploit plant growth-promoting abilities in the native potato microbiota.

Keywords: ecosystem functions; microbiota; potato; rhizosphere.

Figure 1

Influence of the physicochemical composition of sampled localities. A principal component analysis, with a biplot, is shown. The percentage of the variance of the first two components is reported. Overlapped labels on the biplot indicate that they do not contribute to the differences among localities.

Figure 2

Alpha diversity indices of the samples. (a) Shannon index; (b) Simpson index; (c,d) evenness (Camargo‘s and Pielou’s indices, respectively). Lines and the numbers above the lines indicate the p-values of the contrasts (Wilcoxon test).

Figure 3

Nonmetric multidimensional scaling of potato bacterial rhizomicrobiota. Colors indicate locations; circles, flowering stages; triangles, harvesting stages. Stress value = 0.17.

Figure 4

Relative abundances of bacterial phyla in the potato bacterial rhizomicrobiota. The four localities are shown separately. Samples from flowering and harvesting stages are indicated. See Table S1 for sample codes. (a) Gavigno 1. (b) Gavigno 2. (c) Prato. (d) Val di Chiana.

Figure 5

Metabolic pathways mainly contributing to differences among localities (A) and phenological stages (B). See Table S1 for samples codes.