Complete genome sequence of biocontrol strain Bacillus velezensis YC89 and its biocontrol potential against sugarcane red rot

Linyan Xie; Lufeng Liu; Yanju Luo; Xibing Rao; Yining Di; Han Liu; Zhenfeng Qian; Qingqing Shen; Lilian He; Fusheng Li

doi:10.3389/fmicb.2023.1180474

Complete genome sequence of biocontrol strain Bacillus velezensis YC89 and its biocontrol potential against sugarcane red rot

Front Microbiol. 2023 Jun 2:14:1180474. doi: 10.3389/fmicb.2023.1180474. eCollection 2023.

Authors

Linyan Xie¹, Lufeng Liu², Yanju Luo¹, Xibing Rao¹, Yining Di^{2

3}, Han Liu¹, Zhenfeng Qian¹, Qingqing Shen¹, Lilian He^{1

2}, Fusheng Li^{1

2}

Affiliations

¹ College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China.
² College of Resources and Environment, Yunnan Agricultural University, Kunming, China.
³ Sugarcane Research Institute, Yunnan Agricultural University, Kunming, China.

Abstract

Introduction: Sugarcane is one of the most important sugar crops worldwide, however, sugarcane production is seriously limited by sugarcane red rot, a soil-borne disease caused by Colletotrichum falcatum. Bacillus velezensis YC89 was isolated from sugarcane leaves and can significantly inhibited red rot disease caused by C. falcatum.

Methods: In this study, the genome of YC89 strain was sequenced, its genome structure and function were analyzed using various bioinformatics software, and its genome was compared with those of other homologous strains. In addition, the effectiveness of YC89 against sugarcane red rot and the evaluation of sugarcane plant growth promotion were also investigated by pot experiments.

Results: Here, we present the complete genome sequence of YC89, which consists of a 3.95 Mb circular chromosome with an average GC content of 46.62%. The phylogenetic tree indicated that YC89 is closely related to B. velezensis GS-1. Comparative genome analysis of YC89 with other published strains (B. velezensis FZB42, B. velezensis CC09, B. velezensis SQR9, B. velezensis GS-1, and B. amyloliquefaciens DSM7) revealed that the strains had a part common coding sequences (CDS) in whereas 42 coding were unique of strain YC89. Whole-genome sequencing revealed 547 carbohydrate-active enzymes and identified 12 gene clusters encoding secondary metabolites. Additionally, functional analysis of the genome revealed numerous gene/gene clusters involved in plant growth promotion, antibiotic resistance, and resistance inducer synthesis. In vitro pot tests indicated that YC89 strain controlled sugarcane red rot and promoted the growth of sugarcane plants. Additionally, it increased the activity of enzymes involved in plant defense, such as superoxide dismutase, peroxidase, polyphenol oxidase, chitinase, and β-1,3-glucanase.

Discussion: These findings will be helpful for further studies on the mechanisms of plant growth promotion and biocontrol by B. velezensis and provide an effective strategy for controlling red rot in sugarcane plants.

Keywords: Bacillus velezensis; biocontrol; biocontrol mechanism; genome sequencing; sugarcane red rot.