Abstract
The structure of endophytic bacteria is important to plant health and stress tolerance, but little is known about the impacts of farming systems on temporal changes in diversity of endophytic bacteria. In this study, we investigated the endophytic microbiome in rice roots under organic and conventional farming systems at the seedling and tillering stages over two consecutive cropping seasons using 16S rRNA gene sequencing. Although the composition of the microbiome was significantly influenced by a field management system, growth stage, and interaction between the two factors, the growth stage alone explained more than 40% of variance. Soil pH and organic matter content also partially influenced the endophytic bacterial community composition. In addition, through indicator species analysis and the functional profiles predicted by phylogenetic analysis, we revealed the selection force of rice roots at the tillering stage to recruit endophytes, which are beneficial to plant growth. In summary, our data show that the dynamics of rice root bacterial composition are mainly influenced by the plant growth stage. Our findings offer new insights regarding the control of the root microbiome by host plants and the influence of farming systems.
Highlights
The development of the conventional farming system, which relies heavily on chemical fertilizers and control agents, such as pesticides and herbicides, has helped double crop yields and improve food security in the past decades [1]
We investigated the rice root endophytic bacterial microbiome either under conventional or organic farming systems at seedling and tillering stages by using 16S rRNA gene sequencing over two consecutive cropping seasons
Each season the samples included four irrigated rice paddy fields, two of which were managed under a conventional farming system and two of which were managed under an organic farming system
Summary
The development of the conventional farming system, which relies heavily on chemical fertilizers and control agents, such as pesticides and herbicides, has helped double crop yields and improve food security in the past decades [1]. This system has a high impact on agricultural and natural ecosystems [1,2,3,4]. Plant endophytes are defined as microbes isolated or extracted from surface-sterilized tissue [13] Of those microbes that do not cause visible harm, most are commensals but a few are mutualists and have positive effects on plant growth or stress tolerance [14].
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