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Journal of Integrative Agriculture  2016, Vol. 15 Issue (8): 1883-1891    DOI: 10.1016/S2095-3119(15)61195-9
Soil & Fertilization﹒Irrigation﹒Plant Nutrition﹒ Agro-Ecology & Environment Advanced Online Publication | Current Issue | Archive | Adv Search |
Characterization of root-associated bacterial community structures in soybean and corn using locked nucleic acid (LNA) oligonucleotide- PCR clamping and 454 pyrosequencing
YU Zhen-hua1*, YU Jiang1, 2*, Makoto Ikenaga3, Masao Sakai3, LIU Xiao-bing1, WANG Guang-hua1
1 Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, P.R.China
2 College of Agronomy, Northeast Agricultural University, Harbin 150030, P.R.China
3 Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
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Abstract      The community structure and diversity of root-associated bacteria have been tentatively investigated using polymerase chain reaction (PCR) amplification methods in several studies. However, the homology between small submit ribosomal (SSU) rRNA genes of plant plastids and mitochondria and that of bacteria have hindered in these studies. To address this issue, in this paper, we adopted the methods of locked nucleic acid (LNA) oligonucleotide-PCR clamping with 454 pyrosequencing to analysis the root-associated bacterial community compositions in soybean and corn. Results showed that plant chloroplast and mitochondria genes were effectively inhibited from PCR amplification in the root samples with LNA oligonucleotides (LNA (+)), and PCR amplicons with LNA (+) had higher bacterial operational taxonomic unit (OTU) numbers and ACE, Chao1, and Shannon indices, as well as a lower Simpson index than the corresponding samples without LNA oligonucleotides (LNA (–)). Those findings suggested that the methods of this study provide a much more detail description of root-associated bacterial communities. In the soybean LNA (+) sample, Pseudomonas, Bradyrhizobium and Flavobacterium were the three most abundant genera, whereas the top two predominant genera in corn LNA (+) samples were Streptomyces and Niastella. The presence and absence of major genera varied between soybean and corn, suggesting the root-associated bacterial communities differed between two crops. The rare phylotypes and uncultured root-associated bacterial members detected in this study inferred that the root-associated bacterial communities are highly complex and information on their taxonomic affiliates potentially gives the clues for selecting the optimal medium and method to isolate the novel bacteria for further functional analysis.
Keywords:  bacterial diversity        high-throughput sequencing        corn        soybean        SSU rRNA genes  
Received: 26 June 2015   Accepted: 01 August 2016

This work was supported in part by grants from the Strategic Priority Research Program of Chinese Academy of Sciences (XDB15010103) and the National Natural Science Foundation of China (41201247).

Corresponding Authors:  WANG Guang-hua, Tel: +86-451-86602745, Fax: +86-451-86603736, E-mail:; Makoto Ikenaga, Tel: +81-99-2858660, E-mail:   

Cite this article: 

YU Zhen-hua, YU Jiang, Makoto Ikenaga, Masao Sakai, LIU Xiao-bing, WANG Guang-hua. 2016. Characterization of root-associated bacterial community structures in soybean and corn using locked nucleic acid (LNA) oligonucleotide- PCR clamping and 454 pyrosequencing. Journal of Integrative Agriculture, 15(8): 1883-1891.

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