Analysis of soil bacterial communities and physicochemical properties associated with Fusarium wilt disease of banana in Malaysia

Abstract

Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (TR4) is a soil-borne disease that infects bananas, causing severe economic losses worldwide. To reveal the relationship between bacterial populations and FW, the bacterial communities of healthy and TR4-infected rhizosphere and bulk soils were compared using 16S rRNA gene sequencing. Soil physicochemical properties associated with FW were also analyzed. We found the community structure of bacteria in the healthy and TR4 infected rhizosphere was significantly different compared to bulk soil within the same farm. The rhizosphere soils of infected plants exhibited higher richness and diversity than healthy plant with significant abundance of Proteobacteria. In the healthy rhizosphere soil, beneficial bacteria such as Burkholderia and Streptomyces spp. were more abundant. Compared to the infected rhizosphere soil, healthy rhizosphere soil was associated with RNA metabolism and transporters pathways and a high level of magnesium and cation exchange capacity. Overall, we reported changes in the key taxa of rhizospheric bacterial communities and soil physicochemical properties of healthy and FW-infected plants, suggesting their potential role as indicators for plant health.

Figure 1

Relative abundance of bacterial phyla associated with individual soil samples. (a) A color-coded bar plot shows the percentage of major bacterial phyla. The y-axis represents the classification level of phyla, and the x-axis represents the means value in groups. (b) t-test performed at phyla rank for the rhizosphere soil samples. The blue and orange columns represent the average results in the infected and healthy soils, respectively. The colour of the circle agrees with the group whose mean value is higher. The right-most value is the p-value of the significance test between-group variations. Significant differences were shown according to the t-test bar plot taxon rank. BH, bulk soil from healthy plants; BI, bulk soil from infected plants; RH, rhizosphere soil from healthy plant; RI, rhizosphere soil from infected plant.

Figure 2

Alpha diversity of the soil bacterial community according to the (a) Chao1, (b) Observed OTU, (c) Shannon and d) Simpson at OTU level represented as boxplot. Each boxplot represents the diversity distribution of a group present within soil type and pairwise comparison was performed using t-test. Significant differences were accepted when p < 0.05 between the two groups. * denotes p < 0.01 and ** denotes p < 0.001.

Figure 3

Principal coordinate analysis (PCoA) based on Bray–Curtis distance between (a) all soil samples, colored according to soil types (rhizosphere and bulk soils) and (b) healthy (RH) and infected (RI) rhizosphere soils.

Figure 4

Differential abundance of bacterial taxa in the rhizosphere soil samples as determined by LEfSe. (a) Bacterial community between RH and RI at feature-level based on adjusted p- value cutoff = 0.05 with LDA score > 4. (b) Heatmap and hierarchical cluster analysis of bacterial taxa measured using Euclidean distance and Ward linkage clustering algorithm at feature-level based on the relative abundances of biomarker taxa from RH and RI.

Figure 5

Tax4Fun predictions of the functional composition of rhizosphere microbiome of healthy and FW-infected banana. (a) Relative abundances of KEGG functional genes encoded in rhizosphere soils. (b) Differentially abundant KEGG functional genes in RH and RI. LDA effect size (LEfSe) was calculated using LDA with p-value cutoff = 0.05 with LDA score > 3 of KEGG ortholog.