Nitrogen Fertilizer Amendment Alter the Bacterial Community Structure in the Rhizosphere of Rice (Oryza sativa L.) and Improve Crop Yield

Jun Chen; Yasir Arafat; Israr Ud Din; Bo Yang; Liuting Zhou; Juanying Wang; Puleng Letuma; Hongmiao Wu; Xianjin Qin; Linkun Wu; Sheng Lin; Zhixing Zhang; Wenxiong Lin

doi:10.3389/fmicb.2019.02623

Nitrogen Fertilizer Amendment Alter the Bacterial Community Structure in the Rhizosphere of Rice (Oryza sativa L.) and Improve Crop Yield

Front Microbiol. 2019 Nov 14:10:2623. doi: 10.3389/fmicb.2019.02623. eCollection 2019.

Authors

Jun Chen^{1

2

3}, Yasir Arafat^{1

2

4}, Israr Ud Din⁵, Bo Yang^{1

2

3}, Liuting Zhou^{1

2}, Juanying Wang^{1

2}, Puleng Letuma^{2

3}, Hongmiao Wu^{1

2

3}, Xianjin Qin^{2

3}, Linkun Wu^{1

2

3}, Sheng Lin^{1

2}, Zhixing Zhang^{1

2

3}, Wenxiong Lin^{1

2

3}

Affiliations

¹ College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
² Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China.
³ Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China.
⁴ Key Laboratory of Crop Genetic Breeding and Comprehensive Utilization of the Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
⁵ Institute of Biotechnology and Genetic Engineering, The University of Agriculture Peshawar, Peshawar, Pakistan.

Abstract

Availability of nitrogen (N) in soil changes the composition and activities of microbial community, which is critical for the processing of soil organic matter and health of crop plants. Inappropriate application of N fertilizer can alter the rhizosphere microbial community and disturb the soil N homeostasis. The goal of this study was to assess the effect of different ratio of N fertilizer at various early to late growth stages of rice, while keeping the total N supply constant on rice growth performance, microbial community structure, and soil protein expression in rice rhizosphere. Two different N regimes were applied, i.e., traditional N application (NT) consists of three sessions including 60, 30 and 10% at pre-transplanting, tillering and panicle initiation stages, respectively, while efficient N application (NF) comprises of four sessions, i.e., 30, 30, 30, and 10%), where the fourth session was extended to anthesis stage. Soil metaproteomics combined with Terminal Restriction Fragment Length Polymorphism (T-RFLP) were used to determine the rhizosphere biological process. Under NF application, soil enzymes, nitrogen utilization efficiency and rice yield were significantly higher compared to NT application. T-RFLP and qPCR analysis revealed differences in rice rhizosphere bacterial diversity and structure. NF significantly decreased the specific microbes related to denitrification, but opposite result was observed for bacteria associated with nitrification. Furthermore, soil metaproteomics analysis showed that 88.28% of the soil proteins were derived from microbes, 5.74% from plants, and 6.25% from fauna. Specifically, most of the identified microbial proteins were involved in carbohydrate, amino acid and protein metabolisms. Our experiments revealed that NF positively regulates the functioning of the rhizosphere ecosystem and further enabled us to put new insight into microbial communities and soil protein expression in rice rhizosphere.

Keywords: T-RFLP; nitrogen utilization efficiency; rice; soil enzyme; soil metaproteomics.