Effects of an EPSPS-transgenic soybean line ZUTS31 on root-associated bacterial communities during field growth

Abstract

The increased worldwide commercial cultivation of transgenic crops during the past 20 years is accompanied with potential effects on the soil microbial communities, because many rhizosphere and endosphere bacteria play important roles in promoting plant health and growth. Previous studies reported that transgenic plants exert differential effects on soil microbial communities, especially rhizobacteria. Thus, this study compared the soybean root-associated bacterial communities between a 5-enolpyruvylshikimate-3-phosphate synthase -transgenic soybean line (ZUTS31 or simply Z31) and its recipient cultivar (Huachun3 or simply HC3) at the vegetative, flowering, and seed-filling stages. High-throughput sequencing of 16S rRNA gene (16S rDNA) V4 hypervariable region amplicons via Illumina MiSeq and real-time quantitative PCR (qPCR) were performed. Our results revealed no significant differences in the overall alpha diversity of root-associated bacterial communities at the three developmental stages and in the beta diversity of root-associated bacterial communities at the flowering stage between Z31 and HC3 under field growth. However, significant differences in the beta diversity of rhizosphere bacterial communities were found at the vegetative and seed-filling stages between the two groups. Furthermore, the results of next generation sequencing and qPCR showed that the relative abundances of root-associated main nitrogen-fixing bacterial genera, especially Bradyrhizobium in the roots, evidently changed from the flowering stage to the seed-filling stage. In conclusion, Z31 exerts transitory effects on the taxonomic diversity of rhizosphere bacterial communities at the vegetative and seed-filling stages compared to the control under field conditions. In addition, soybean developmental change evidently influences the main symbiotic nitrogen-fixing bacterial genera in the roots from the flowering stage to the seed-filling stage.

Impact of a <i>G2-EPSPS</i> & <i>GAT</i> Dual Transgenic Glyphosate-Resistant Soybean Line on the Soil Microbial Community under Field Conditions Affected by Glyphosate Application

“…The general concept of the present study was partly derived from previous studies (Mendes et al, 2014;Edwards et al, 2015) that examined the microbial communities associated with three rhizo-compartments. In the present study, we used similar compartments, including the surrounding soil, rhizospheric soil and associated roots containing the rhizoplane and endosphere (Bulgarelli et al, 2012;Edwards et al, 2015;Lu et al, 2018b;Wen et al, 2019), to effectively compare differences among the three soybean treatments at the three growth stages and assess the impact of GM crops on underground microbial communities.…”

“…The root sample (RT) (a mixed sample of the rhizoplane/ endosphere and the layer of endophytes in roots) was collected after washing with phosphate-buffered saline (PBS) (Lu et al, 2017). All samples were then stored at 4°C for a basic physicochemical analysis and at -80°C for DNA extraction (Lu et al, 2018a(Lu et al, , 2018b.…”

“…At the seed filling stage, total qualified paired-end clean reads were 2,989,410 and the average count per sample was 87,924 (range: 49,695-145,012) (Table S1). Operational taxonomic units (OTUs) were selected as previously described (Lu et al, 2018a(Lu et al, , 2018b with minor modifications. Chimeras were filtered out using UCHIME (v4.2.40) and connected tags were filtered to eliminate low quality and short sequences using QIIME (v1.7.0) before clean tags were obtained (Edgar et al, 2011;Edgar, 2013).…”

“…Chimeras were filtered out using UCHIME (v4.2.40) and connected tags were filtered to eliminate low quality and short sequences using QIIME (v1.7.0) before clean tags were obtained (Edgar et al, 2011;Edgar, 2013). As described previously by Lu et al (Lu et al, 2018a, 2018b, OTU counts in each sample's library were normalized after species annotation and phylogenetic tree construction, mitochondrion/chloroplast-related sequences (phylum Cyanobacteria, family Mitochondria) from the sequence data set were simultaneously removed, and all of the operations described above were conducted in the I-Sanger platform (http://www.i-sanger.com). Alpha and beta diversity analyses were then conducted based on OTUs and species annotation results (Wen et al, 2019).…”

Enrichments/Derichments of Root-Associated Bacteria Related to Plant Growth and Nutrition Caused by the Growth of an EPSPS-Transgenic Maize Line in the Field

“…To date, high-throughput next-generation sequencing (NGS) technologies, such as 454 GS FLX pyrosequencing, with its corresponding bioinformatics tools, are widely used in the research of soil microbial communities (Inceoglu et al, 2011; Bulgarelli et al, 2012, 2013; Lundberg et al, 2012; Peiffer et al, 2013; Schlaeppi et al, 2014). Meanwhile, the Illumina MiSeq platform has emerged as another powerful NGS technology for its far more cost-effective advantage and has been performed by many researchers for studying the highly complicated microbial communities (Kozich et al, 2013; Schmidt et al, 2013; Bakker et al, 2015; Edwards et al, 2015; Yang et al, 2015; Lu et al, 2018).…”