Fusarium Wilt Invasion Results in a Strong Impact on Strawberry Microbiomes

Abstract

Plant-endophytic microbes affect plant growth, development, nutrition, and resistance to pathogens. However, how endophytic microbial communities change in different strawberry plant compartments after Fusarium pathogen infection has remained elusive. In this study, 16S and internal transcribed spacer rRNA amplicon sequencing were used to systematically investigate changes in the bacterial and fungal diversity and composition in the endophytic compartments (roots, stems, and leaves) of healthy strawberries and strawberries with Fusarium wilt, respectively. The analysis of the diversity, structure, and composition of the bacterial and fungal communities revealed a strong effect of pathogen invasion on the endophytic communities. The bacterial and fungal community diversity was lower in the Fusarium-infected endophytic compartments than in the healthy samples. The relative abundance of certain bacterial and fungal genera also changed after Fusarium wilt infection. The relative abundance of the beneficial bacterial genera Bacillus, Bradyrhizobium, Methylophilus, Sphingobium, Lactobacillus, and Streptomyces, as well as fungal genera Acremonium, Penicillium, Talaromyces, and Trichoderma, were higher in the healthy samples than in the Fusarium wilt samples. The relative abundance of Fusarium in the infected samples was significantly higher than that in the healthy samples, consistent with the field observations and culture isolation results for strawberry wilt. Our findings provide a theoretical basis for the isolation, identification, and control of strawberry wilt disease.

Keywords: bacterial community; fungal community; microbiome; plant pathogen; strawberry Fusarium wilt disease.

Figure 1

Alpha diversity of bacterial (A,B) and fungal (C,D) communities in the roots, stems, and leaves of healthy strawberry plants and strawberries with Fusarium wilt. Diversity estimated using Shannon’s index (A,C) and Chao1 index (B,D). Statistical analysis conducted using Student’s t test (* p < 0.05, ** p < 0.01, and *** p < 0.001). HR: root samples of healthy strawberry plants; IR: root samples of infected strawberry plants; HS: stem samples of healthy strawberry plants; IS: stem samples of infected strawberry plants; HL: leaf samples of healthy strawberry plants; IL: leaf samples of infected strawberry plants.

Figure 2

Principal coordinate analysis (PCoA) of bacterial (A) and fungal (B) communities in healthy strawberry plants and strawberries with Fusarium wilt, with Bray–Curtis dissimilarities. Analysis of similarities (ANOSIM) conducted to test for differences in community composition resulting from compartment and health status. R values are presented and labeled with asterisks: ** p < 0.01 and *** p < 0.001.

Figure 3

Relative abundance of most abundant (>0.1%) bacterial phyla and Proteobacteria classes (−) (A) and fungal phyla and Ascomycetes classes (−) (B) in each compartment between healthy strawberries and strawberries with Fusarium wilt. Student’s t test used to identify significant differences between healthy strawberries and strawberries with Fusarium wilt (* p < 0.05, ** p < 0.01, and *** p < 0.001). HR: root samples of healthy strawberry plants; IR: root samples of infected strawberry plants; HS: stem samples of healthy strawberry plants; IS: stem samples of infected strawberry plants; HL: leaf samples of healthy strawberry plants; IL: leaf samples of infected strawberry plants.

Figure 4

Relative abundance of dominant bacterial (A) and fungal (B) genera in roots, stems, and leaves of healthy strawberries and strawberries with Fusarium wilt (10 replicates). Figure depicts bacterial and fungal genera with relative abundance of >0.3%. Cell colors represent log₂ fold change in relative abundance compared with control treatment, with brown indicating increasing trend and cyan indicating decreasing trend. (C) Relative abundance of the fungal genera Fusarium. Student’s t test revealed significant differences in relative abundance of bacterial (A) and fungal (B) genus and Fusarium (C) (* p < 0.05, ** p < 0.01, and *** p < 0.001) between healthy strawberries and strawberries with Fusarium wilt (n = 10). HR: root samples of healthy strawberry plants; IR: root samples of infected strawberry plants; HS: stem samples of healthy strawberry plants; IS: stem samples of infected strawberry plants; HL: leaf samples of healthy strawberry plants; IL: leaf samples of infected strawberry plants.

Figure 5

Relative abundance of bacterial (A) and fungal (B) predicted functional groups (guilds) in healthy and infected roots, stems, and leaves inferred using PICRUSt2 and FUNGuild, respectively. Student’s t test revealed significant differences in relative abundance of bacterial metabolic function and fungal functional guilds (* p < 0.05, ** p < 0.01, and *** p < 0.001) between healthy strawberries and strawberries with Fusarium wilt (n = 10). HR: root samples of healthy strawberry plants; IR: root samples of infected strawberry plants; HS: stem samples of healthy strawberry plants; IS: stem samples of infected strawberry plants; HL: leaf samples of healthy strawberry plants; IL: leaf samples of infected strawberry plants.

Figure 6

(A) Venn diagram of common and unique fungal species isolated using tissue separation from healthy and infected roots, stems, and leaves. (B) Relative abundance of fungal species Fusarium oxysporum. (C) Relative abundance of fungal species isolated from healthy and infected roots, stems, and leaves. HR: root samples of healthy strawberry plants; IR: root samples of infected strawberry plants; HS: stem samples of healthy strawberry plants; IS: stem samples of infected strawberry plants; HL: leaf samples of healthy strawberry plants; IL: leaf samples of infected strawberry plants.