Rhizobium Symbiotic Capacity Shapes Root-Associated Microbiomes in Soybean

Yuanhui Liu; Bin Ma; Wenfeng Chen; Klaus Schlaeppi; Matthias Erb; Erinne Stirling; Lingfei Hu; Entao Wang; Yunzeng Zhang; Kankan Zhao; Zhijiang Lu; Shudi Ye; Jianming Xu

doi:10.3389/fmicb.2021.709012

Rhizobium Symbiotic Capacity Shapes Root-Associated Microbiomes in Soybean

Front Microbiol. 2021 Dec 2:12:709012. doi: 10.3389/fmicb.2021.709012. eCollection 2021.

Authors

Yuanhui Liu^{1

2

3}, Bin Ma^{1

2

4}, Wenfeng Chen⁵, Klaus Schlaeppi^{6

7}, Matthias Erb⁷, Erinne Stirling^{1

2

4

8}, Lingfei Hu^{1

2}, Entao Wang⁹, Yunzeng Zhang¹⁰, Kankan Zhao^{1

2}, Zhijiang Lu^{1

2}, Shudi Ye^{1

2}, Jianming Xu^{1

2}

Affiliations

¹ Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
² Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.
³ China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China.
⁴ Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China.
⁵ State Key Laboratory of Agrobiotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Ministry of Agriculture Key Laboratory of Soil Microbiology, Beijing, China.
⁶ Department of Environmental Sciences, University of Basel, Basel, Switzerland.
⁷ Institute of Plant Sciences, University of Bern, Bern, Switzerland.
⁸ Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
⁹ Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, México.
¹⁰ College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China.

Abstract

Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes is that they engage in symbiosis with N₂-fixing rhizobia. If and how the rhizobial symbiotic capacity modulates root-associated microbiomes are still not yet well understood. We determined root-associated microbiomes of soybean inoculated with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens USDA 110 by amplicon sequencing. UPLC-MS/MS was used to analyze root exudates. The noeI gene is responsible for fucose-methylation of Nod factor secreted by USDA 110 WT strain. Soybean roots inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation compared to roots inoculated with WT strain. The noeI mutant-inoculated roots exhibited strong changes in microbiome assembly in the rhizosphere and rhizoplane, including reduced diversity, changed co-occurrence interactions and a substantial depletion of root microbes. Root exudates and soil physiochemical properties were significantly correlated with microbial community shift in the rhizosphere between different rhizobial treatments. These results illustrate that rhizobial symbiotic capacity dramatically alters root-associated microbiomes, in which root exudation and edaphic patterns play a vital role. This study has important implications for understanding the evolution of plant-microbiome interactions.

Keywords: Glycine max; rhizobia; root exudation; root-associated microbiome; symbiosis.