Comparative Analysis of the Microbial Community Structures Between Healthy and Anthracnose-Infected Strawberry Rhizosphere Soils Using Illumina Sequencing Technology in Yunnan Province, Southwest of China

Daifa Su; Shanyan Chen; Wenxing Zhou; Junyu Yang; Zhiwei Luo; Zhenrong Zhang; Yunxia Tian; Qionge Dong; Xuemei Shen; Shijie Wei; Jiangyun Tong; Xiaolong Cui

doi:10.3389/fmicb.2022.881450

Comparative Analysis of the Microbial Community Structures Between Healthy and Anthracnose-Infected Strawberry Rhizosphere Soils Using Illumina Sequencing Technology in Yunnan Province, Southwest of China

Front Microbiol. 2022 May 16:13:881450. doi: 10.3389/fmicb.2022.881450. eCollection 2022.

Authors

Daifa Su^{1

2}, Shanyan Chen³, Wenxing Zhou³, Junyu Yang^{1

2}, Zhiwei Luo³, Zhenrong Zhang³, Yunxia Tian³, Qionge Dong³, Xuemei Shen³, Shijie Wei³, Jiangyun Tong³, Xiaolong Cui^{1

2}

Affiliations

¹ Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China.
² State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
³ Kunming Academy of Agricultural Science, Kunming, China.

Abstract

Anthracnose caused by Colletotrichum spp. was widespread in recent years and resulted in great damage to strawberry production. Soil microbial communities were key contributors to host nutrition, development, and immunity; however, the difference between the microbial communities of healthy and anthracnose-infected strawberry rhizosphere soils remains unclear. In this study, the Illumina sequencing technique was used to comparatively study the prokaryotic and fungal community compositions and structures between healthy and anthracnose-infected strawberry rhizosphere soils in Yuxi, Yunnan Province. Both microbial community diversities and richness of anthracnose-infected strawberry rhizosphere soils were higher than those of healthy strawberry rhizosphere soils. A total of 2,518 prokaryotic and 556 fungal operational taxonomic units (OTUs) were obtained at the 97% similarity threshold. Proteobacteria, Thaumarchaeota, and Acidobacteria were the dominant prokaryotic phyla; Ascomycota, unclassified_k__Fungi, and Mortierellomycota were the dominant fungal phyla. The relative abundances of beneficial bacterial phyla Actinobacteria and Firmicutes, genera Streptomyces, Azospirillum, and Bacillus were significantly reduced in anthracnose-infected strawberry rhizosphere soils; the relative abundance of beneficial fungal species Trichoderma asperellum shows a similar tendency with bacterial abundance. Besides Colletotrichum, 15 other potential fungal pathogen genera and seven fungal pathogen species were identified; among the potential pathogen genera and species, eight pathogen genera and Fusarium oxysporum showed significant differences between healthy and anthracnose-infected strawberry rhizosphere soils. The results suggested that strawberry planted in this area may be infected by other fungal pathogens except for Colletotrichum spp. Our present research will provide theoretical basis and data reference for the isolation and identification of strawberry pathogens and potential probiotics in future works.

Keywords: cultivated strawberry; high-throughput sequencing technology; microbial community; rhizosphere soil; strawberry anthracnose.