Impact of a Glyphosate-Tolerant Soybean Line on the Rhizobacteria, Revealed by Illumina MiSeq |
Lu, Gui-Hua
(NJU-NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University)
Zhu, Yin-Ling (NJU-NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University) Kong, Ling-Ru (NJU-NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University) Cheng, Jing (NJU-NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University) Tang, Cheng-Yi (NJU-NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University) Hua, Xiao-Mei (Nanjing Institute of Environmental Sciences, MEP) Meng, Fan-Fan (Jilin Academy of Agricultural Sciences) Pang, Yan-Jun (NJU-NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University) Yang, Rong-Wu (NJU-NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University) Qi, Jin-Liang (NJU-NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University) Yang, Yong-Hua (NJU-NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University) |
1 | James C. 2015. Global status of commercialized biotech/GM crops: 2014. China Biotechnol. 35: 1-14. |
2 | Padgette SR, Kolacz KH, Delannay X, Re DB, Lavallee BJ, Tinius CN, et al. 1995. Development, identification, and characterization of a glyphosate-tolerant soybean line. Crop Sci. 35: 1451-1461. DOI |
3 | Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75: 7537-7541. DOI |
4 | Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7: 335-336. DOI |
5 | Zhou J, Wu L, Deng Y, Zhi X, Jiang YH, Tu Q, et al. 2011. Reproducibility and quantitation of amplicon sequencingbased detection. ISME J. 5: 1303-1313. DOI |
6 | White JR, Nagarajan N, Pop M. 2009. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput. Biol. 5: e1000352. DOI |
7 | Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate-a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Stat. Methodol. 57: 289-300. |
8 | Weaver MA, Krutz LJ, Zablotowicz RM, Reddy KN. 2007. Effects of glyphosate on soil microbial communities and its mineralization in a Mississippi soil. Pest Manag. Sci. 63: 388-393. DOI |
9 | Kremer RJ, Means NE. 2009. Glyphosate and glyphosateresistant crop interactions with rhizosphere microorganisms. Eur. J. Agron. 31: 153-161. DOI |
10 | Wang Z, Liu ZH, Wang HY. 2012. Salinization resistance transgenic soybean reduced bacterial diversity in rhizosphere. Adv. Intel. Soft. Comput. 134: 377-384. |
11 | Aira M, Gomez-Brandon M, Lazcano C, Baath E, Dominguez J. 2010. Plant genotype strongly modifies the structure and growth of maize rhizosphere microbial communities. Soil Biol. Biochem. 42: 2276-2281. DOI |
12 | Nakatani AS, Fernandes MF, de Souza RA, da Silva AP, dos Reis FB, Mendes IC, Hungria M. 2014. Effects of the glyphosate-resistance gene and of herbicides applied to the soybean crop on soil microbial biomass and enzymes. Field Crops Res. 162: 20-29. DOI |
13 | Lugtenberg B, Kamilova F. 2009. Plant-growth-promoting rhizobacteria. Annu. Rev. Microbiol. 63: 541-556. DOI |
14 | Berendsen RL, Pieterse CMJ, Bakker PAHM. 2012. The rhizosphere microbiome and plant health. Trends Plant Sci. 17: 478-486. DOI |
15 | Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EVL, Schulze-Lefert P. 2013. Structure and functions of the bacterial microbiota of plants. Annu. Rev. Plant Biol. 64: 807-838. DOI |
16 | Berg G, Smalla K. 2009. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol. Ecol. 68: 1-13. DOI |
17 | Inceoglu O, Salles JF, van Overbeek L, van Elsas JD. 2010. Effects of plant genotype and growth stage on the betaproteobacterial communities associated with different potato cultivars in two fields. Appl. Environ. Microbiol. 76: 3675-3684. DOI |
18 | Ofek M, Voronov-Goldman M, Hadar Y, Minz D. 2014. Host signature effect on plant root-associated microbiomes revealed through analyses of resident vs. active communities. Environ. Microbiol. 16: 2157-2167. DOI |
19 | Liang JG, Sun S, Ji J, Wu HY, Meng F, Zhang MR, et al. 2014. Comparison of the rhizosphere bacterial communities of zigongdongdou soybean and a high-methionine transgenic line of this cultivar. PLoS One 9: e103343. DOI |
20 | Peiffer JA, Spor A, Koren O, Jin Z, Tringe SG, Dangl JL, et al. 2013. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc. Natl. Acad. Sci. USA 110: 6548-6553. DOI |
21 | Dunfield KE, Germida JJ. 2001. Diversity of bacterial communities in the rhizosphere and root interior of fieldgrown genetically modified Brassica napus. FEMS Microbiol. Ecol. 38: 1-9. DOI |
22 | Arango L, Buddrus-Schiemann K, Opelt K, Lueders T, Haesler F, Schmid M, et al. 2014. Effects of glyphosate on the bacterial community associated with roots of transgenic Roundup Ready (R) soybean. Eur. J. Soil Biol. 63: 41-48. DOI |
23 | Newman MM, Hoilett N, Lorenz N, Dick RP, Liles MR, Ramsier C, Kloepper JW. 2016. Glyphosate effects on soil rhizosphere-associated bacterial communities. Sci. Total Environ. 543: 155-160. DOI |
24 | Siciliano SD, Germida JJ. 1999. Taxonomic diversity of bacteria associated with the roots of field-grown transgenic Brassica napus cv. Quest, com pared to the non-transgenic B. napus cv. Excel and B. rapa cv. Parkland. FEMS Microbiol. Ecol. 29: 263-272. DOI |
25 | Dunfield KE, Germida JJ. 2003. Seasonal changes in the rhizosphere microbial communities associated with fieldgrown genetically modified canola (Brassica napus). Appl. Environ. Microbiol. 69: 7310-7318. DOI |
26 | Jin J, Wang GH, Liu XB, Liu JD, Chen XL, Herbert SJ. 2009. Temporal and spatial dynamics of bacterial community in the rhizosphere of soybean genotypes grown in a black soil. Pedosphere 19: 808-816. DOI |
27 | Kondorosi E, Mergaert P, Kereszt A. 2013. A paradigm for endosymbiotic life: cell differentiation of Rhizobium bacteria provoked by host plant factors. Annu. Rev. Microbiol. 67: 611-628. DOI |
28 | Xu YX, Wang GH, Jin J, Liu JJ, Zhang QY, Liu XB. 2009. Bacterial communities in soybean rhizosphere in response to soil type, soybean genotype, and their growth stage. Soil Biol. Biochem. 41: 919-925. DOI |
29 | Li CG, Li XM, Kong WD, Wu Y, Wang JG. 2010. Effect of m onoculture s oybean o n soil m icrobial c omm unity in t he Northeast China. Plant Soil 330: 423-433. DOI |
30 | Yang T, Liu G, Li Y, Zhu S, Zou A, Qi J, Yang Y. 2012. Rhizosphere microbial communities and organic acids secreted by aluminum-tolerant and aluminum-sensitive soybean in acid soil. Biol. Fertil. Soils 48: 97-108. DOI |
31 | Masson-Boivin C, Giraud E, Perret X, Batut J. 2009. Establishing nitrogen-fixing symbiosis with legumes: how many Rhizobium recipes? Trends Microbiol. 17: 458-466. DOI |
32 | Berg G, Grube M, Schloter M, Smalla K. 2014. Unraveling the plant microbiome: looking back and future perspectives. Front. Microbiol. 5: article 148. |
33 | Ryan RP, Monchy S, Cardinale M, Taghavi S, Crossman L, Avison MB, et al. 2009. The versatility and adaptation of bacteria from the genus Stenotrophomonas. Nat. Rev. Microbiol. 7: 514-525. DOI |
34 | Chen Y, Duan R, Li X, Li K, Liang J, Liu C, et al. 2015. Homology analysis and cross-immunogenicity of OmpA from pathogenic Yersinia enterocolitica, Yersinia pseudotuberculosis and Yersinia pestis. Mol. Immunol. 68: 290-299. DOI |
35 | Taghavi S, Garafola C, Monchy S, Newman L, Hoffman A, Weyens N, et al. 2009. Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees. Appl. Environ. Microbiol. 75: 748-757. DOI |
36 | Muller H, Furnkranz M, Grube M, Berg G. 2013. Genome sequence of Serratia plymuthica strain S13, an endophyte with germination-and plant-growth-promoting activity from the flower of Styrian oil pumpkin. Genome Announc. 1: e00594. |
37 | Gans J, Wolinsky M, Dunbar J. 2005. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387-1390. DOI |
38 | Dunfield KE, Germida JJ. 2004. Impact of genetically modified crops on soil-and plant-associated microbial communities. J. Environ. Qual. 33: 806-815. DOI |
39 | Liu B, Zeng Q, Yan FM, Xu HG, Xu CR. 2005. Effects of transgenic plants on soil microorganisms. Plant Soil 271: 1-13. DOI |
40 | Turrini A, Sbrana C, Giovannetti M. 2015. Belowground environmental effects of transgenic crops: a soil microbial perspective. Res. Microbiol. 166: 121-131. DOI |
41 | Inceoglu O, Abu Al-Soud W, Salles JF, Semenov AV, van Elsas JD. 2011. Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing. PLoS One 6: e23321. DOI |
42 | Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. 2013. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq illumina sequencing platform. Appl. Environ. Microbiol. 79: 5112-5120. DOI |
43 | Tang CY, Yang MK, Wu FY, Zhao H, Pang YJ, Yang RW, et al. 2015. Identification of miRNAs and their targets in transgenic Brassica napus and its acceptor (Westar) by highthroughput sequencing and degradome analysis. RSC Adv. 5: 85383-85394. DOI |
44 | Lin WY, Huang TK, Chiou TJ. 2 013. Nitrogen limitation adaptation, a target of microRNA827, mediates degradation of plasma membrane-localized phosphate transporters to maintain phosphate homeostasis in Arabidopsis. Plant Cell 25: 4061-4074. DOI |
45 | Bulgarelli D, Rott M, Schlaeppi K, van Themaat EVL, Ahmadinejad N, Assenza F, et al. 2012. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488: 91-95. DOI |
46 | Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, et al. 2012. Defining the core Arabidopsis thaliana root microbiome. Nature 488: 86-90. DOI |
47 | Schlaeppi K, Dombrowski N, Oter RG, van Themaat EVL, Schulze-Lefert P. 2014. Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc. Natl. Acad. Sci. USA 111: 585-592. DOI |
48 | Schmidt PA, Balint M, Greshake B, Bandow C, Rombke J, Schmitt I. 2013. Illumina metabarcoding of a soil fungal community. Soil Biol. Biochem. 65: 128-132. DOI |
49 | Yang CY, Li Y, Zhou B, Zhou YY, Zheng W, Tian Y, et al. 2015. Illumina sequencing-based analysis of free-living bacterial community dynamics during an Akashiwo sanguine bloom in Xiamen sea, China. Sci. Rep. 5: 8476. DOI |
50 | Bakker MG, Chaparro JM, Manter DK, Vivanco JM. 2015. Impacts of bulk soil microbial community structure on rhizosphere microbiomes of Zea mays. Plant Soil 392: 115-126. DOI |
51 | Magoc T, Salzberg SL. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27: 2957-2963. DOI |
52 | Edwards J, Johnson C, Santos-Medellin C, Lurie E, Podishetty NK, Bhatnagar S, et al. 2015. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl. Acad. Sci. USA 112: E911-E920. DOI |
53 | Kennedy K, Hall MW, Lynch MDJ, Moreno-Hagelsieb G, Neufeld JD. 2014. Evaluating bias of illumina-based bacterial 16S rRNA gene profiles. Appl. Environ. Microbiol. 80: 5717-5722. DOI |
54 | Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J. 2014. An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the illumina MiSeq platform. Microbiome 2: article 6. |
55 | Edgar RC. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10: 996-998. DOI |
56 | Cole JR, Wang Q, Fish JA, Chai BL, McGarrell DM, Sun YN, et al. 2014. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42: D633-D642. DOI |
57 | DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72: 5069-5072. DOI |
58 | Chen H, Boutros PC. 2011. VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics 12: 35. DOI |
![]() |