Comparison of bacterial communities in soil samples with and without tomato bacterial wilt caused by Ralstonia solanacearum species complex

Abstract

Background: Ralstonia solanacearum is one of the most notorious soil-borne phytopathogens. It causes a severe wilt disease with deadly effects on many economically important crops. The microbita of disease-suppressive soils are thought that they can contribute to the disease resistance of crop plants, thus, evaluation of the microbial community and their interaction characteristics between suppressive soil (SS) and conducive soil (CS) will help to understand resistance mechanism. To do this, the bacterial community structure, correlation analysis with soil chemical properties, interaction network of SS (nearly no disease in three years), and CS (suffered heavy bacterial wilt disease) were analyzed.

Results: A higher bacterial community diversity index was found in SS, the relative abundance of Nocardioides, Gaiella and norank_f_Anaerolineaceae were significantly more than that of the CS. Moreover, the relative abundance of main genera Bacillus, norank_o_Gaiellales, Roseiflexus, and norank_o_Gemmatimonadaceae were significantly more than that of the CS. Redundancy analysis at the genus level indicated that the available phosphate played a key role in the bacterial community distribution, and its role was negatively correlated with soil pH, organic matter content, alkali-hydrolyzable nitrogen, and available potassium contents. Interaction network analysis further demonstrated that greater diversity at the genus level existed in the SS network and formed a stable network. Additionally, the species of Mycobacterium, Cyanobacteria, and Rhodobiaceae are the key components that sustain the network stability. Seven clusters of orthologous groups exhibited significant differences between SS and CS. Moreover, 55 bacterial strains with distinct antagonistic activities to R. solancearum were isolated and identified from the healthy tomato plant rhizosphere soil of the CS.

Conclusions: Our findings indicate that the bacterial diversity and interaction network differed between the CS and SS samples, providing a good foundation in the study of bacterial wilt.

Keywords: Biological control; Conducive soils; Interaction network; Ralstonia solanacearum; Rhizosphere bacteria; Suppressive soils; Tomato.

Fig. 1

Venn analysis of shared and unique OTUs between suppressive soil (SS) and conducive soil (CS) samples a. OTUs defined by 97% sequence similarity and Student’s t-test of OTU level between suppressive soil (SS) and conducive soil (CS) b. **p ≤ 0.01

Fig. 2

Community bar plot analysis of five suppressive soil (SS) samples (SS1, SS2, SS3, SS4, and SS5) and five conducive soil (CS) samples (CS1, CS2, CS3, CS4, and CS5) at the genus level. “Others” indicates genera with the relative abundance lower than 0.1%. The x-axis of the column is the percentage relative abundance at the genus level

Fig. 3

PCoA analysis at the genus level between suppressive soil (SS) and conducive soil (CS). The β-diversity was calculated based on the Bray-Curtis algorithm

Fig. 4

Welch’s t-test and FDR comparison analysis of microbial communities at the genus level between suppressive soil (SS) and conducive soil (CS). The Scheffe’s value cutoff was 0.95, ***p ≤ 0.001, **0.001 < p ≤ 0.01, and *0.01 < p ≤ 0.05

Fig. 5

Correlations analysis between bacterial diversity (genus level) and soil chemical properties of suppressive soil (SS) and conducive soil (CS). The green arrows represent genus, red arrows represent environmental factors (EF): soil pH, organic matter (OM), alkali-hydrolyzable nitrogen (AHN), rapidly available phosphate (RAP), and rapidly available potassium (RAK). The length of the red arrows indicates the degree of impact by related EF, the angle between EF represents positive or negative correlation, the acute angle represents positive correlation, the obtuse angle represents negative correlation, and the right angle represents no correlation

Fig. 6

Interaction network analysis at the genus level of suppressive soil (SS) a and conducive soil (CS) b. Different node colors represent different bacteria genera. Blue lines represent negative interactions; red lines represent positive interactions among different nodes

Fig. 7

Significantly different COGs between suppressive soil (SS) and conducive soil (CS). S: function unknown; H: coenzyme transport and metabolism; A: RNA processing and modification; F: nucleotide transport and metabolism; D: cell cycle control, cell division, chromosome partitioning; C: energy production and conversion; Z: cytoskeleton