Enrichment of potentially beneficial bacteria from the consistent microbial community confers canker resistance on tomato

Jiakang Yin; Youfeng Yu; Ziliang Zhang; Lingling Chen; Lifang Ruan

doi:10.1016/j.micres.2020.126446

Enrichment of potentially beneficial bacteria from the consistent microbial community confers canker resistance on tomato

Microbiol Res. 2020 Feb 22:234:126446. doi: 10.1016/j.micres.2020.126446. Online ahead of print.

Authors

Jiakang Yin¹, Youfeng Yu¹, Ziliang Zhang¹, Lingling Chen², Lifang Ruan³

Affiliations

¹ State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.
² National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China.
³ State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China. Electronic address: ruanlifang@mail.hzau.edu.cn.

PMID: 32126507
DOI: 10.1016/j.micres.2020.126446

Abstract

The soil microbiota interacts with plants closely and exerts strong influences on plant health and productivity. However, the relationship between the microbiota and the bacterial canker of tomato that is caused by Clavibacter michiganensis subsp. michiganensis (Cmm) is still unclear. In order to establish causal relationship between the microbiota and plant phenotypes, the microbial communities of 49 tomato samples (including 15 cultivars) with different canker symptoms collected from the greenhouse in Gansu province, China were investigated via 16S ribosomal RNA sequencing. Roots exhibited a strong filter effect in the process of root colonization by microorganisms according to the α-diversity and the separation patterns of the microbiota in bulk soil, rhizosphere and endosphere. In addition, the gradually decreased cluster extent from bulk soil to endosphere indicating the selective effect of tomato on microbiota. Although the composition of the microbiota is similar, the potential beneficial bacteria and functions (e.g. antibiotics production, pollution degradation, nutrition acquisition) enriched in the rhizosphere and endosphere of healthy samples compared to those in the diseased ones. Furthermore, more robust networks occurred in the rhizosphere and endosphere of healthy samples compared to the diseased ones. Our research provided substantial evidence that although the plant genotype is the dominant factor of phenotype, the rhizosphere and endosphere microbiota, as part of phytobiomes or holobiont, could contribute to the host's phenotype. This causal relationship between microbiota and host phenotypes could guide us in rationally designing novel synthetic communities (SynComs) for tomato canker biocontrol in the near future.

Keywords: Microbiota; Phenotype; Phytobiome; Tomato bacterial canker.