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Gigascience. 2017 Oct 1;6(10):1-12. doi: 10.1093/gigascience/gix089.

Taxonomic structure and functional association of foxtail millet root microbiome.

Author information

BGI-Qingdao, Qingdao, 266510, China.
China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China.
Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA.
BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.
State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China.
Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark.
BGI Millet Co., Ltd, Shenzhen, 518083, China.
James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, 100101, China.
Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Science & John Innes Centre, Beijing, 100101, China.
The University of Chinese Academy of Sciences, Beijing, 100049, China.


The root microbes play pivotal roles in plant productivity, nutrient uptakes, and disease resistance. The root microbial community structure has been extensively investigated by 16S/18S/ITS amplicons and metagenomic sequencing in crops and model plants. However, the functional associations between root microbes and host plant growth are poorly understood. This work investigates the root bacterial community of foxtail millet (Setaria italica) and its potential effects on host plant productivity. We determined the bacterial composition of 2882 samples from foxtail millet rhizoplane, rhizosphere and corresponding bulk soils from 2 well-separated geographic locations by 16S rRNA gene amplicon sequencing. We identified 16 109 operational taxonomic units (OTUs), and defined 187 OTUs as shared rhizoplane core OTUs. The β-diversity analysis revealed that microhabitat was the major factor shaping foxtail millet root bacterial community, followed by geographic locations. Large-scale association analysis identified the potential beneficial bacteria correlated with plant high productivity. Besides, the functional prediction revealed specific pathways enriched in foxtail millet rhizoplane bacterial community. We systematically described the root bacterial community structure of foxtail millet and found its core rhizoplane bacterial members. Our results demonstrated that host plants enrich specific bacteria and functions in the rhizoplane. The potentially beneficial bacteria may serve as a valuable knowledge foundation for bio-fertilizer development in agriculture.


16S rRNA; Setaria italica; microbiome; productivity; root

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