Different rhizosphere soil microbes are recruited by tomatoes with different fruit color phenotypes

Abstract

Background: To explore and utilize abundant soil microbes and their beneficial functions, the bacterial and fungal compositions in rhizospheres between red- and yellow-fruited tomato varieties were analyzed using high-throughput sequencing technique.

Result: Our results indicated that different soil microbes in rhizospheres of tomatoes were exactly recruited by different color fruit tomatoes. For the reasons as not only soil bacterial community, but also soil fungal compositions were all different between red and yellow fruit tomatoes. For example, Nocardioides, norank_f_norank_o_Vicinamibacterales, norank_f_norank_o_norank_c_KD4-96, norank_f_Birii41, norank_f_norank_o_S085 and Bradyrhizobium were the specific dominant soil bacterial genera, and Lecythophora, Derxomyces and unclassified_f_Pyronemataceae were the dominant soil fungal genera in the rhizospheres of red tomato varieties. By contrast, unclassified_f__Micromonsporaceae, Acidipila, Roseisolibacter, Gaiella and norank_f_Xanthobacteraceae were the unique dominant soil bacterial genera in the rhizospheres of yellow tomato varieties. And unclassified_o__Onygenales, Trichocladium, unclassified_c__Sordariomycetes, Pseudogymnoascus, Acremonium, Oidiodendron, Phialemonium, Penicillium, Phialosimplex were the unique dominant soil fungal genera in rhizospheres of yellow tomato varieties. Moreover, a higher abundance of specific soil bacterial and fungal genera in the rhizosphere was found in rhizospheres of the yellow than those of the red tomato varieties.

Conclusion: Soil bacterial and fungal compositions in rhizospheres between red- and yellow-fruited tomato varieties were found significantly different which growing in the same environment under the identical managements. It suggested that different soil microbes in rhizospheres exactly were recruited by different phenotypes tomato varieties related to fruit color formation.

Keywords: Bacteria; Fruit color; Fungi; Rhizosphere; Tomato.

Fig. 1

Proportion of dominant rhizosphere soil bacteria for yellow- (Y) and red-fruited tomatoes (R) and background soil (CK). a: Soil bacteria at the phylum classification level; (b): Soil bacteria at the genus classification level

Fig. 2

Venn diagram of soil bacteria among CK and the rhizospheres of yellow- (Y) and red-fruited (R) tomato varieties; (a): Soil bacteria at the genus level; (b): Soil bacteria at the OTU level

Fig. 3

Difference test of dominant soil bacteria in rhizospheres at the phylum among CK and the rhizospheres of yellow- (Y) and red-fruited (R) tomato varieties *0.01 < p ≤ 0.05, **0.001 < p ≤ 0.01, ***p ≤ 0.001

Fig. 4

Difference test of dominant soil bacteria in the rhizosphere at the genus level among CK and the rhizospheres of yellow- (Y) and red-fruited (R) tomato varieties; *0.01 < p ≤ 0.05, **0.001 < p ≤ 0.01, ***p ≤ 0.001

Fig. 5

Lefse analysis of significant bacteria among CK and the rhizospheres of yellow- (Y) and red-fruited (R) tomato varieties

Fig. 6

Co-occurrence network analysis of soil bacteria in rhizospheres of different tomato varieties; The red line indicates a positive interaction, the green line indicates a negative interaction, and marked nodes represent significant differences, p < 0.05

Fig. 7

Proportion of dominant rhizosphere fungi in yellow-fruited tomato (Y), red-fruited tomato (R), and background soil (CK), (a): Soil fungi at the phylum classification level; (b): Soil fungi at the genus classification level

Fig. 8

Venn diagram of soil fungi among CK and rhizospheres of yellow-(Y) and red (R)-fruited tomato varieties, (a): Soil fungi at the genus level;(b): Soil fungi at the OTU level

Fig. 9

Lefse analysis of significant fungi among CK and the rhizospheres of yellow- (Y) and red-fruited tomatoes (R)

Fig. 10

Co-occurrence network analysis of soil fungi in rhizospheres of different tomato varieties; The red line indicates a positive interaction, the green line indicates a negative interaction, and marked nodes represent significant differences, p < 0.05

Fig. 11

The appearance and morphological characteristics of the tomato varieties with different fruit colors