Changes in bacterial community and abundance of functional genes in paddy soil with cry1Ab transgenic rice

doi:10.1016/S2095-3119(20)63271-3

摘要/Abstract

摘要：

自2014年起建立了转cry1Ab基因水稻（GM）及其对照非转基因水稻（M）的田间试验。分别利用16S rRNA基因的Illumina MiSeq 高通量测序及amoA, nirS和 nirK基因的实时定量PCR，分析了田间试验第五年稻田土壤细菌群落和驱动氮素转化的功能基因丰度的变化。结果显示：转基因水稻GM的土壤细菌群落的a多样性指数，包括物种丰富度指数Chao1、香农多样性指数Shannon和辛普森多样性指数Simpson，在水稻各个生育期内均与非转基因水稻M间没有差异。但是基于unweighted UniFrac距离的主坐标分析(Principal coordinates analysis，PCoA)和非度量多维尺度分析(Nonmetric Multidimensional scaling，NMDS)显示，转基因水稻GM的细菌群落与非转基因水稻M在水稻各个生育期内均存在分布差异。且基于unweighted UniFrac距离的ADONIS和ANOSIM分析结果表明上述GM与M的细菌群落分布差异都达到显著性水平(P<0.05)。GM土壤中酸杆菌门 Acidobacteria和M土壤中拟杆菌门Bacteroidetes相对丰度的增加可导致其细菌群落的差异。同时，高通量测序的基因功能预测结果显示，在水稻成熟期转基因水稻GM土壤中一些功能基因丰度提高，如与淀粉、氨基酸和氮代谢相关的基因。此外，转基因水稻GM土壤中的氨氧化细菌amoA基因、氨氧化古菌amoA基因及反硝化细菌nirK基因的丰度均显著增加(P<0.05 或 0.01)。总之，转cry1Ab基因水稻对土壤细菌群落组成和微生物功能基因丰度均存在影响。

Abstract:

A field experiment involving cry1Ab transgenic rice (GM) and its parental non-cry1Ab rice (M) has been on-going since 2014. The diversity of the bacterial communities and the abundance of the microbial functional genes which drive the conversion of nitrogen in paddy soil were analyzed during the growth period of rice in the fifth year of the experiment, using 16S rRNA-based Illumina MiSeq and real-time PCR on the amoA, nirS and nirK genes. The results showed no differences in the alpha diversity indexes of the bacterial communities, including Chao1, Shannon and Simpson, between the fields cultivated with line GM and cultivar M at any of the growth stages of rice. However, the bacterial communities in the paddy soil with line GM were separated from those of paddy soil with cultivar M at each of the growth stages of rice, based on the unweighted UniFrac NMDS or PCoA. In addition, the analyses of ADONIS and ANOSIM, based on the unweighted UniFrac distance, indicated that the above separations between line GM and cultivar M were statistically significant (P<0.05) during the growth season of rice. The increases in the relative abundances of Acidobacteria or Bacteroidetes, in the paddy soils with line GM or cultivar M, respectively, led to the differences in the bacterial communities between them. At the same time, functional gene prediction based on Illumina MiSeq data suggested that the abundance of many functional genes increased in the paddy soil with line GM at the maturity stage of rice, such as genes related to the metabolism of starch, amino acids and nitrogen. Otherwise, the copies of bacterial amoA gene, archaeal amoA gene and denitrifying bacterial nirK gene significantly increased (P<0.05 or 0.01) in the paddy soil with line GM. In summary, the release of cry1Ab transgenic rice had effects on either the composition of bacterial communities or the abundance of microbial functional genes in the paddy soil.

Key words: cry1Ab transgenic rice , bacterial community , microbial functional gene , Illumina MiSeq Platform , real-time PCR

. [J]. Journal of Integrative Agriculture, 2021, 20(6): 1674-1686.

SONG Ya-na, CHEN Zai-jie, WU Ming-ji, LI Gang, WANG Feng. Changes in bacterial community and abundance of functional genes in paddy soil with cry1Ab transgenic rice[J]. Journal of Integrative Agriculture, 2021, 20(6): 1674-1686.

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