Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach

Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China

Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China

State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, MEP, Nanjing 210042, China

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Jilin Academy of Agricultural Sciences, Changchun 130033, China

Authors to whom correspondence should be addressed.

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These authors contributed equally to this work.

Genes 2018, 9(4), 214; https://doi.org/10.3390/genes9040214

Received: 22 January 2018 / Revised: 19 March 2018 / Accepted: 13 April 2018 / Published: 16 April 2018

(This article belongs to the Special Issue Emerging Applications for Next Generation Sequencing)

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Abstract

The worldwide commercial cultivation of transgenic crops, including glyphosate-tolerant (GT) soybeans, has increased widely during the past 20 years. However, it is accompanied with a growing concern about potential effects of transgenic crops on the soil microbial communities, especially on rhizosphere bacterial communities. Our previous study found that the GT soybean line NZL06-698 (N698) significantly affected rhizosphere bacteria, including some unidentified taxa, through 16S rRNA gene (16S rDNA) V4 region amplicon deep sequencing via Illumina MiSeq. In this study, we performed 16S rDNA V5–V7 region amplicon deep sequencing via Illumina MiSeq and shotgun metagenomic approaches to identify those major taxa. Results of these processes revealed that the species richness and evenness increased in the rhizosphere bacterial communities of N698, the beta diversity of the rhizosphere bacterial communities of N698 was affected, and that certain dominant bacterial phyla and genera were related to N698 compared with its control cultivar Mengdou12. Consistent with our previous findings, this study showed that N698 affects the rhizosphere bacterial communities. In specific, N698 negatively affects Rahnella, Janthinobacterium, Stenotrophomonas, Sphingomonas and Luteibacter while positively affecting Arthrobacter, Bradyrhizobium, Ramlibacter and Nitrospira. View Full-Text

Keywords: soil; rhizosphere; glyphosate-tolerant soybean; 16S rRNA gene; plant growth-promoting rhizobacteria; shotgun metagenomic approach

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Doi: https://doi.org/10.4014/jmb.1609.09008
Link: http://www.jmb.or.kr/submission/Journal/027/JMB027-03-16_FSUP_1.pdf
Description: Table S10 Differ_rela_abundance of rhizosphere bacterial genera between N698&MD12

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Lu, G.-H.; Hua, X.-M.; Liang, L.; Wen, Z.-L.; Du, M.-H.; Meng, F.-F.; Pang, Y.-J.; Qi, J.-L.; Tang, C.-Y.; Yang, Y.-H. Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach. Genes 2018, 9, 214. https://doi.org/10.3390/genes9040214

AMA Style

Lu G-H, Hua X-M, Liang L, Wen Z-L, Du M-H, Meng F-F, Pang Y-J, Qi J-L, Tang C-Y, Yang Y-H. Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach. Genes. 2018; 9(4):214. https://doi.org/10.3390/genes9040214

Chicago/Turabian Style

Lu, Gui-Hua, Xiao-Mei Hua, Li Liang, Zhong-Ling Wen, Mei-Hang Du, Fan-Fan Meng, Yan-Jun Pang, Jin-Liang Qi, Cheng-Yi Tang, and Yong-Hua Yang. 2018. "Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach" Genes 9, no. 4: 214. https://doi.org/10.3390/genes9040214

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Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach

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