Soil acidification amendments change the rhizosphere bacterial community of tobacco in a bacterial wilt affected field

Abstract

Application of soil amendments has been wildly used to increase soil pH and control bacterial wilt. However, little is known about causal shifts in the rhizosphere microbial community of crops, especially when the field naturally harbors the disease of bacterial wilt to tobacco for many years due to long-term continuous cropping and soil acidification. In this study, biochar (CP), lime (LM), oyster shell powder (OS) and no soil amendment additions (Control; CK) were assessed for their abilities to improve the soil acidification, change the composition of rhizosphere soil bacterial communities and thus control tobacco bacterial wilt. The results showed that oyster shell powder significantly increased soil pH by 0.77 and reduced the incidence of tobacco bacterial wilt by 36.67% compared to the control. The Illumina sequencing -based community analysis showed that soil amendment applications affected the composition of rhizosphere bacterial community and increased the richness and diversity. In contrast, the richness and diversity correlated negatively to disease incidence. Using LEfSe analyses, 11 taxa were found to be closely related with disease suppression, in which Saccharibacteria, Aeromicrobium, and Pseudoxanthomonas could be potential indicators of disease suppression. Our results suggested that the suppression of bacterial wilt after the application of soil amendments (especially oyster shell powder) was attributed to the improved soil pH and increased bacterial richness and diversity.

Keywords: Bacterial wilt; Microbial community; Oyster shell powder; Soil amendments; Soil pH.

Fig. 1

Disease incidence of tobacco bacterial wilt (a) and soil pH (b) in each treatment. Letters above the bars indicate a significant difference according to Tukey’s multiple comparison test at the P < 0.05 level

Fig. 2

PCoA plot based on Bray-Curtis distances of microbial communities sampled from each treatment

Fig. 3

Bacterial community structure in the four treated soils at the phylum level. Other phyla represent < 1% of the total reads. Statistical significance (P < 0.05) using Tukey’s multiple comparison test is designated by an asterisk

Fig. 4

Bacterial community structure in the four treated soils at the family level. Other families represent < 2% of the total reads. Statistical significance (P < 0.05) using Tukey’s multiple comparison test is designated by an asterisk

Fig. 5

Cladogram indicating the phylogenetic distribution of bacterial lineages under each treatment: a biochar (CP), b lime LM, c oyster shell powder (OS), and control groups (CK); lineages with LDA values higher than 2.0 are displayed. d Venn diagram for biochar (94), lime (43), and oyster shell powder groups (62) screened out from LEfSe analyses at the genus level, and the shared 11 taxa are shown in Table 2

Fig. 6

Linear regression analysis of the relationship between tobacco bacterial wilt rate and alpha-diversity. The alpha-diversity: a Shannon index, b Simpson index, c Chao index, and d ACE index