Biological influence of cry1Ab gene insertion on the endophytic bacteria community in transgenic rice

The commercial release of genetically modified (GMO) rice for insect control in China is a subject of debate. Although a series of studies have focused on the safety evaluation of the agroecosystem, the endophytes of transgenic rice are rarely considered. Here, the influence of endophyte populations and communities was investigated and compared for transgenic and nontransgenic rice. Population-level investigation suggested that cry1Ab gene insertion influenced to a varying degree the rice endophytes at the seedling stage, but a significant difference was only observed in leaves of Bt22 (Zhejiang22 transgenic rice) between the GMO and wild-type rice. Community-level analysis using the 16S rRNA gene showed that strains of the phyla Proteobacteria and Firmicutes were the predominant groups occurring in the three transgenic rice plants and their corresponding parents. By contrast, the endophytic communities of Minghui63 and Xiushui11 showed a weaker response to cry1Ab gene insertion than did Zhejiang22, and the community results were consistent with the population-level investigation. The populations and communities of rice endophytes were affected by the cry1Ab gene to a different extent in different rice varieties and plant tissues. The results of this study broaden our understanding of unexpected transgenic influences on nontarget organisms.

Keywords:

16S rRNA community structure, endophytes, transgenic rice,

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Ansari MR, Shaheen T, Bukhari SA, Husnain T (2015). Genetic improvement of rice for biotic and abiotic stress tolerance. Turk J Bot 39: 911-919.
Bevilacqua M, Marini F (2014). Local classification: locally weighted- partial least squares-discriminant analysis (LW-PLS-DA). Anal Chim Acta 838: 20-30.
Brosius J, Palmer ML, Kennedy PJ, Noller HF (1978). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . P Natl Acad Sci USA 75: 4801-4805.
Bruto M, Prigent-Combaret C, Muller D, Moenne-Loccoz Y (2014). Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related Proteobacteria. Sci Rep 4: 6261.
Chen M, Shelton A, Ye GY (2011). Insect-resistant genetically modified rice in China: from research to commercialization. Annu Rev Endomol 56: 81-101.
Chen Q, Yang B, Liu X, Chen F, Ge F (2017). Long-term cultivation of Bt rice expressing the Cry1Ab/1Ac gene reduced phytoparasitic nematode abundance but did not affect other nematode parameters in paddy fields. Sci Total Environ 607-608: 463-474.
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed- Mohideen AS, McGarrell DM, Marsh T, Garrity GM et al. (2009). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141- 145.
Craig W, Tepfer M, Degrassi G, Ripandelli D (2008). An overview of general features of risk assessments of genetically modified crops. Euphytica 164: 853-880.
Dale PJ, Clarke B, Fontes EM (2002). Potential for the environmental impact of transgenic crops. Nat Biotechnol 20: 567-574.
Feng Y, Shen D, Song W (2006). Rice endophyte Pantoea agglomerans YS19 promotes host plant growth and affects allocations of host photosynthates. J Appl Microbiol 100: 938-945.
FAO (2008). FAO and Sustainable Intensification of Rice Production for Food Security. Rome, Italy: FAO.
Hall TA (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT. Nucl Acid S 96: 95-98.
Hallmann J, Quadt-Hallmann A, Rodríguez-Kábana R, Kloepper JW (1998). Interactions between Meloidogyne incognita and endophytic bacteria in cotton and cucumber. Soil Biol Biochem 30: 925-937.
Khush GS (2005). What it will take to feed 5.0 billion rice consumers in 2030. Plant Mol Biol 59: 1-6.
Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, Wassmann R, von Mering C, Vorholt JA (2012). Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J 6: 1378-1390.
Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007). Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . Int J Syst Evol Microbiol 57: 1424-1428.
Liu Y, Li J, Luo Z, Wang H, Liu F (2016). The fate of fusion Cry1Ab/1Ac proteins from Bt-transgenic rice in soil and water. Ecotoxicol Environ Saf 124: 455-459.
Lodewyck C, Vangronsveld J, Porteous F, Moore ERB, Taghavi S, Mezgeay M, van der Lelie D (2002). Endophytic bacteria and their potential application. Crit Rev Plant Sci 86: 583-606.
Ma B, Lv X, Warren A, Gong J (2013). Shifts in diversity and community structure of endophytic bacteria and archaea across root, stem and leaf tissues in the common reed, Phragmites australis , along a salinity gradient in a marine tidal wetland of northern China. Anton Leeuw Int J G 104: 759-768.
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P (2012). An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6: 610-618.
MAPRC (2009). The Second List of Approval: Agricultural Genetically Modified Organisms’ Safety Certificates in 2009. Beijing, China: Ministry of Agriculture of the People’s Republic of China (in Chinese).
Oyebanji OB, Nweke O, Odebunmi O, Galadima NB, Galadima NB, Idris MS, Nnodi UN, Afolabi AS, Ogbadu GH (2009). Simple, effective and economical explant-surface sterilization protocol for cowpea, rice and sorghum seeds. Afr J Biotechnol 8: 5395- 5399.
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO (2007). SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
Rangjaroen C, Sungthong R, Rerkasem B, Teaumroong N, Noisangiam R, Lumyong S (2017). Untapped endophytic colonization and plant growth-promoting potential of the genus Novosphingobium to optimize rice cultivation. Microbes Environ 32: 84-87.
Saxena D, Stotzky G (2001). Bacillus thuringiensis ( Bt ) toxin released from root exudates and biomass of Bt corn has no apparent effect on earthworms, nematodes, protozoa, bacteria, and fungi in soil. Soil Biol Biochem 33: 1225-1230.
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ et al. (2009). Introducing mothur: open-source, platform- independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
Shu Y, Zhang Y, Zeng H, Zhang Y, Wang J (2017). Effects of Cry1Ab Bt maize straw return on bacterial community of earthworm Eisenia fetida . Chemosphere 173: 1-13.
Singh AK, Singh M, Dubey SK (2013). Changes in Actinomycetes community structure under the influence of Bt transgenic brinjal crop in a tropical agroecosystem. BMC Microbiol 13: 122.
Sun L, Qiu F, Zhang X, Dai X, Dong X, Song W (2008). Endophytic bacterial diversity in rice ( Oryza sativa L.) roots estimated by 16S rDNA sequence analysis. Microb Ecol 55: 415-424.
Zhu W, Lu H, Hill J, Guo X, Wang H, Wu W (2014). 13 C pulse-chase labeling comparative assessment of the active methanogenic archaeal community composition in the transgenic and nontransgenic parental rice rhizospheres. FEMS Microbiol Ecol 87: 746-56.
Zwahlen C, Hilbeck A, Gugerli P, Nentwig W (2003). Degradation of the Cry1Ab protein within transgenic Bacillus thuringiensis corn tissue in the field. Mol Ecol 12: 765-775.