Environmental factors shaping the diversity of bacterial communities that promote rice production

Zhaohui Wu,Huaqun Yin,Ping Lei,Qingshu Liu,Jimin Sun,Yongmei Li,Zhenyu Li,Hongbo Li,Jianqun Zhou,Delong Meng,Wei Cheng,Zhaohui Guo

doi:10.1186/s12866-018-1174-z

Abstract

BackgroundExploiting soil microorganisms in the rhizosphere of plants can significantly improve agricultural productivity; however, the mechanism by which microorganisms specifically affect agricultural productivity is poorly understood. To clarify this uncertainly, the rhizospheric microbial communities of super rice plants at various growth stages were analysed using 16S rRNA high-throughput gene sequencing; microbial communities were then related to soil properties and rice productivity.ResultsThe rhizospheric bacterial communities were characterized by the phyla Proteobacteria, Acidobacteria, Chloroflexi, and Verrucomicrobia during all stages of rice growth. Rice production differed by approximately 30% between high- and low-yield sites that had uniform fertilization regimes and climatic conditions, suggesting the key role of microbial communities. Mantel tests showed a strong correlation between soil conditions and rhizospheric bacterial communities, and microorganisms had different effects on crop yield. Among the four growing periods, the rhizospheric bacterial communities present during the heading stage showed a more significant correlation (p < 0.05) with crop yield, suggesting their potential in regulating crop production. The biological properties (i.e., microbes) reflected the situation of agricultural land better than the physicochemical characterics (i.e., nutrient elements), which provides theoretical support for agronomic production. Molecular ecological network (MEN) analysis suggested that differences in productivity were caused by the interaction between the soil characteristics and the bacterial communities.ConclusionsDuring the heading stage of rice cropping, the rhizospheric microbial community is vital for the resulting rice yield. According to network analysis, the cooperative relationship (i.e., positive interaction) between between microbes may contribute significantly to yield, and the biological properties (i.e., microbes) better reflected the real conditions of agricultural land than did the physicochemical characteristics (i.e., nutrient elements).

Highlights

Exploiting soil microorganisms in the rhizosphere of plants can significantly improve agricultural productivity; the mechanism by which microorganisms affect agricultural productivity is poorly understood
The Detrended correspondence analysis (DCA) based on soil environmental factors (Fig. 1) showed the low-yield site had very different soil properties compared to the high-yield sites
total nitrogen (TN), TP, and soil organic matter (SOM) were significantly correlated (p < 0.05) with crop yield in all Bacterial diversity The microbial community diversity indices, including Shannon and Simpson diversity and Pielou evenness were significantly higher in the high-yield sites than in the low-yield site, and generally, the diversity indices were the highest during the tillering stage

Summary

Introduction

Exploiting soil microorganisms in the rhizosphere of plants can significantly improve agricultural productivity; the mechanism by which microorganisms affect agricultural productivity is poorly understood To clarify this uncertainly, the rhizospheric microbial communities of super rice plants at various growth stages were analysed using 16S rRNA high-throughput gene sequencing; microbial communities were related to soil properties and rice productivity. Soil microbial communities drive globally important processes [24], including elemental cycles and energy flows These microbial communities are involved in various processes that serve essential functions in agricultural production [25] by promoting crop absorption of nutrients and inhibiting harmful pathogens [7, 8, 26,27,28]. Explaining the direct effects of soil microbial communities on crop-growth and yield is challenging because the ecosystem functions provides by most soil microorganisms are not well clear [30, 31]. The innate mechanism of how microorganisms affect crop productivity is poorly understood, and our study is devoted to statistically explaining the links between them

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Discussion

Conclusion