High-throughput sequencing analysis of microbial community diversity in response to indica and japonica bar-transgenic rice paddy soils

Abstract

Potential environmental risks of genetically modified (GM) crops have raised concerns. To better understand the effect of transgenic rice on the bacterial community in paddy soil, a field experiment was carried out using pairs of rice varieties from two subspecies (indica and japonica) containing bar transgene with herbicide resistance and their parental conventional rice. The 16S rRNA gene of soil genomic DNA from different soil layers at the maturity stage was sequenced using high-throughput sequencing on the Illumina MiSeq platform to explore the microbial community diversity among different rice soils. There were no significant differences in diversity indices between transgenic japonica rice and its sister conventional rice (japonica pair) among different soil layers, but, significant differences was observed between transgenic indica rice and its conventional rice (indica pair) in the topsoil layer around concentrated rice roots according to the ace diversity index. Though the japonica rice soil and indica rice soil were shared several key genera, including Rivibacter, Anaeromyxobacter, Roseomonas, Geobacter, Thiobacillus, Clostridium, and Desulfobulbus, the primary bacterial genera in indica rice soil were different from those in japonica rice. Synechococcus and Dechloromonas were present in japonica rice samples, while Chloronema, Flexibacter, and Blastocatella were observed in indica rice soil. Moreover, the abundance of genera between GM and non-GM varieties in japonica rice was significantly different from indica rice, and several bacterial communities influenced these differences. Anaerovorax was more abundant in transgenic japonica rice soil than conventional rice soil, while it was deficient in transgenic indica rice soil compared to conventional rice soil, and opposite responses to Deferrisoma were in that of indica rice. Thus, we concluded that transgenic indica and japonica rice had different effects on soil bacteria compared with their corresponding sister conventional rice. However, these composition and abundance difference only occurred for a few genera but had no effect on the primary genera and soil characteristics were mainly contributed to these differences. Thus, differences in bacterial community structure can be ignored when evaluating the impacts of transgenic rice in the complex soil microenvironment.

Steel slag amendment impacts on soil microbial communities and activities of rice (Oryza sativa L.)

“…Noteworthy, large differences in nutrient uptake between Indica and Japonica rice species, even without the slag amendment were observed. Rice species or cultivar variation has been reported to alter rhizosphere microbial community composition and nutrient cycling 37,38 . Plant species with high growth rate have higher rates of root exudation and labile compounds that can fuel rhizosphere microbial community 37,38 .…”

“…Rice species or cultivar variation has been reported to alter rhizosphere microbial community composition and nutrient cycling 37,38 . Plant species with high growth rate have higher rates of root exudation and labile compounds that can fuel rhizosphere microbial community 37,38 . The mantel test analysis revealed that RMC, MBC, aqSi, aqFe, straw and root biomass, and N, P, and Si uptake (straw only) significantly correlated with rhizosphere bacterial communities in control (without slag) treatments (Table 4).…”

Cable bacteria at oxygen‐releasing roots of aquatic plants: a widespread and diverse plant–microbe association

“…Criteria to choose public datasets for analysis were studies that involved next generation sequencing of the 16S rRNA gene of the microbial community in root‐associated or paddy soil samples. Raw sequences and metadata from 21 public datasets (Nguyen et al ., 2015 ; Cúcio et al ., 2016 ; Rothenberg et al ., 2016 ; Shao et al ., 2016 ; Ettinger et al ., 2017 ; Fahimipour et al ., 2017 ; Crump et al ., 2018 ; Edwards et al ., 2018 ; Gong et al ., 2018 ; Kumar et al ., 2018 ; Liu et al ., 2018 ; Martin et al ., 2019 , 2018a , 2018b , 2020 , 2019 , 2018a , 2018b , 2020 ; He et al ., 2019 ; Hurtado‐McCormick et al ., 2019 ; Lin et al ., 2019 ; Ugarelli et al ., 2019 ; Zhu et al ., 2019 ; Ma et al ., 2020 ) and two unpublished projects (Middleton et al ., Ling et al .) including root and bulk samples of aquatic macrophytes (408 samples) and rice (1763 samples) were retrieved from the NCBI database and the Genome Sequence Archive ( https://bigd.big.ac.cn/gsa/ ; Table S1 ).…”

Transgenic Rice Plants Expressing Artificial miRNA Targeting the Rice Stripe Virus MP Gene Are Highly Resistant to the Virus

“…Our marker-gene-free transgenic rice plants contain only the antiviral miRNA and exhibit 90% resistance to RSV infection. As a large number of virus-resistant transgenic crops have emerged, the biological safety of transgenic plants has raised concerns, including off-target effects [ 44 , 45 ]. However, since the transgenic plants express only a short sequence through amiRNA-mediated strategies, these potential risks are likely to be minimal [ 11 ].…”