Impact of Glyphosate on the Rhizosphere Microbial Communities of An EPSPS-Transgenic Soybean Line ZUTS31 by Metagenome Sequencing

Abstract

Background: The worldwide use of glyphosate has dramatically increased, but also has been raising concern over its impact on mineral nutrition, plant pathogen, and soil microbiota. To date, the bulk of previous studies still have shown different results on the effect of glyphosate application on soil rhizosphere microbial communities.

Objective: This study aimed to clarify whether glyphosate has impact on nitrogen-fixation, pathogen or disease suppression, and rhizosphere microbial community of a soybean EPSPS-transgenic line ZUTS31 in one growth season.

Method: Comparative analysis of the soil rhizosphere microbial communities was performed by 16S rRNA gene amplicons sequencing and shotgun metagenome sequencing analysis between the soybean line ZUTS31 foliar sprayed with diluted glyphosate solution and those sprayed with water only in seed-filling stage.

Results: There were no significant differences of alpha diversity but with small and insignificant difference of beta diversity of soybean rhizosphere bacteria after glyphosate treatment. The significantly enriched Gene Ontology (GO) terms were cellular, metabolic, and single-organism of biological process together with binding, catalytic activity of molecular function. The hits and gene abundances of some functional genes being involved in Plant Growth-Promoting Traits (PGPT), especially most of nitrogen fixation genes, significantly decreased in the rhizosphere after glyphosate treatment.

Conclusion: Our present study indicated that the formulation of glyphosate-isopropylamine salt did not significantly affect the alpha and beta diversity of the rhizobacterial community of the soybean line ZUTS31, whereas it significantly influenced some functional genes involved in PGPT in the rhizosphere during the single growth season.

Keywords: 16S rRNA gene amplicons sequencing; EPSPS-transgenic soybean line; Glyphosate; Rhizosphere bacterial community; Shotgun metagenome sequencing; Soil.

Fig. (1)

Principal Component Analysis (PCA) based on OTU abundances of bacterial communities. X-axis was 1st principal component and Y-axis was 2nd principal component. Numbers in brackets represented contributions of principal components to the total variance. A) The black rhombuses and black triangles represented rhizosphere soil replicates of the glyphosate treated Z31J1 and its control Z31, respectively. B) The black squares and the black solid circles represented surrounding soil replicates of glyphosate treated Z31J1 and its control Z31, respectively.

Fig. (2)

Principal Coordinate Analysis (PCoA) based on weighted UniFrac distance. The variance explained by each principal coordinate axis was shown in PCo1 vs. PCo3 and PCo3 vs. PCo2. A) The black rhombuses and black triangles represented rhizosphere soil replicates of the glyphosate treated Z31J1 and its control Z31, respectively. B) The black dots and the dark gray squares represented surrounding soil replicates of glyphosate treated Z31J1 and its control Z31, respectively.

Fig. (3)

Scatter plots of genes with differential abundance. Y and X axis presented value of genes abundance of MGZ31J1DRh and of MGZ31DRh, respectively, based on the assembled data by IDBA-UD. Orange triangles and blue rhombuses indicated genes with significantly higher and lower relative abundance in MGZ31J1DRh, respectively. Brown circles indicate those genes with no significant difference between MGZ31J1DRh and MGZ31DRh. The criterion of screening is on top of the plot. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this paper.)

Fig. (4)

GO functional classification for the pairwise of MGZ31DRh VS MGZ31J1DRh. X-axis means number of genes with different abundance based on data assembled by IDBA-UD. Y-axis represents different GO terms. All GO terms were grouped into three ontologies: the dark gray, gray and black color indicated biological process, cellular component, and molecular function, respectively. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this paper.)