Deciphering microbial diversity associated with Fusarium wilt-diseased and disease-free banana rhizosphere soil

Abstract

Background: Fusarium wilt of banana (Musa spp.) caused by the fungal pathogen Fusarium oxysporum f. sp. cubense (Foc) is a typical soilborne disease, that severely devastates the banana industry worldwide, and soil microbial diversity is closely related to the spread of Fusarium wilt. To understand the relationship between microbial species and Fusarium wilt, it is important to understand the microbial diversity of the Fusarium wilt-diseased and disease-free soils from banana fields.

Results: Based on sequencing analysis of the bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) sequences, Foc abundance, fungal or bacterial richness and diversity were higher in the diseased soils than in the disease-free soils. Although Ascomycota and Zygomycota were the most abundant fungi phyla in all soil samples, Ascomycota abundance was significantly reduced in the disease-free soils. Mortierella (36.64%) was predominant in the disease-free soils. Regarding bacterial phyla, Proteobacteria, Acidobacteria, Chloroflexi, Firmicutes, Actinobacteria, Gemmatimonadetes, Bacteroidetes, Nitrospirae, Verrucomicrobia and Planctomycetes were dominant phyla in all soil samples. In particular, Firmicutes contributed 16.20% of the total abundance of disease-free soils. At the bacterial genus level, Bacillus, Lactococcus and Pseudomonas were abundant in disease-free soils with abundances of 8.20, 5.81 and 2.71%, respectively; lower abundances, of 4.12, 2.35 and 1.36%, respectively, were found in diseased soils. The distribution characteristics of fungal and bacterial genera may contribute to the abundance decrease of Foc in the disease-free soils.

Conclusion: Unique distributions of bacteria and fungi were observed in the diseased and disease-free soil samples from banana fields. These specific genera are useful for constructing a healthy microbial community structure of soil.

Keywords: Bacterial and fungal communities; Banana Fusarium wilt; Environmental variables; Pathogen abundance.

Fig. 1

Number of the pathogen Fusarium oxysporum f. sp. cubense in different soil samples. HB, NB and XB represent the diseased soil samples collected from Huangtong, Nanbao and Xinying farms, respectively. HJ, NJ and XJ represent the disease-free soil samples collected from Huangtong, Nanbao and Xinying farms, respectively. The data in each column is the average value of three replicates (n = 10). The letter on each bar represents a significant difference at the 5% level

Fig. 2

Rarefaction analysis of the diseased and disease-free soil samples at a 3% dissimilarity level. HB, NB, XB, HJ, NJ and XJ were described in Fig. 1. Each sample had three replicates (n = 10)

Fig. 3

Venn diagram of bacterial disease and disease-free soil samples from the three different farms. Diseased soil samples (XB + HB + NB) and disease-free soil samples (XJ + HJ + NJ) were collected from different farms. The shared and unique bacteria OTUs were shown at a 0.03 dissimilarity distance after removing singletons

Fig. 4

Venn diagram for fungal disease and disease-free soil samples from the three different farms. Diseased soil samples (XB + HB + NB) and disease-free soil samples (XJ + HJ + NJ) were collected from different farms. The shared and unique fungus OTUs were shown at a 0.03 dissimilarity distance after removing singletons

Fig. 5

Construction of hierarchical cluster trees using a weighted UniFace algorithm for the diseased and the disease-free soil samples. Each sample has three replicates. a hierarchical cluster tree of bacteria; b abundance of bacterial community at the level of genus; c hierarchical cluster tree of fungi; d abundance of fungal community at the level of genus. “Others” indicate the abundance of less than 2% of genus

Fig. 6

Analysis of abundance differences between the diseased soil samples and the disease-free soil samples at the bacterial genus. a richness differences of bacterial genus; b richness differences of bacterial phylum; c richness differences of fungal genus; d richness differences of fungal phylum. The y-axis represents the classification levels of species, and the x-axis represents the percentage values of species abundance in each sample. The blue and red columns represent the average results in the diseased and disease-free soil samples, respectively. Significant differences were showed according to the Wilcoxon rank-sum test (*: 0.01 < P < =0.05, **: 0.001 < P < =0.01, ***: P < =0.001)

Fig. 7

Analysis of the correlation between microorganisms and environmental variables in both types of soil samples at the level of genus. Mircoorganisms at the level of genus. a bacteria; b fungi. Environmental variables: pH,AP,AK,TOC,TON