Transcriptome sequencing reveals the effect of biochar improvement on the development of tobacco plants before and after topping


Autoři: Shen Yan aff001;  Zhengyang Niu aff001;  Haitao Yan aff001;  Aigai Zhang aff001;  Guoshun Liu aff001
Působiště autorů: Department of Tobacco cultivation, College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan Province, China aff001;  Henan Biochar Engineering Technology Research Center, Zhengzhou, Henan Province, China aff002;  Henan Biochar Technology Engineering Laboratory, Zhengzhou, Henan Province, China aff003;  Department of Microbiology, College of Agriculture and Life Science, Cornell University, Ithaca, NY, United States of America aff004
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: 10.1371/journal.pone.0224556

Souhrn

The application of biochar is one of the most useful methods for improving soil quality, which is of the utmost significance for the continuous production of crops. As there are no conclusive studies on the specific effects of biochar application on tobacco quality, this study aimed to improve the yield and quality of tobacco as a model crop for economic and genetic research in southern China, by such application. We used transcriptome sequencing to reveal the effects of applied biochar on tobacco development before and after topping. Our results showed that topping affected carbon and nitrogen metabolism, photosynthesis and secondary metabolism in the tobacco plants, while straw biochar-application to the soil resulted in amino acid and lipid synthesis; additionally, it affected secondary metabolism of the tobacco plants through carbon restoration and hormonal action, before and after topping. In addition to the new insights into the impact of biochar on crops, our findings provide a basis for biochar application measures in tobacco and other crops.

Klíčová slova:

Amino acid metabolism – Biosynthesis – Gene expression – Metabolic pathways – Metabolic processes – Nicotiana – Nitrogen metabolism – Straw


Zdroje

1. Li H, Dai MW, Dai SL, Dong XJ. Current status and environment impact of direct straw return in China's cropland—A review. Ecotox Environ Safe. 2018;159:293–300.

2. Li H, Cao Y, Wang XM, Ge X, Li BQ, Jin CQ. Evaluation on the Production of Food Crop Straw in China from 2006 to 2014. Bioenerg Res. 2017;10(3):949–57.

3. Lu F. How can straw incorporation management impact on soil carbon storage? A meta-analysis. Mitig Adapt Strat Gl. 2015;20(8):1545–68.

4. Zhu KW, Liu Z, Tan XC, Lin JC, Xu DH. Study on the ecological potential of Chinese straw resources available for bioenergy producing based on soil protection functions. Biomass Bioenerg. 2018;116:26–38.

5. Yang HS, Xu MM, Koide RT, Liu Q, Dai YJ, Liu L, et al. Effects of ditch-buried straw return on water percolation, nitrogen leaching and crop yields in a rice-wheat rotation system. J Sci Food Agr. 2016;96(4):1141–9.

6. Christian DG, Bacon ETG, Brockie D, Glen D, Gutteridge RJ, Jenkyn JF. Interactions of straw disposal methods and direct drilling or cultivations on winter wheat (Triticum aestivum) grown on a clay soil. J Agr Eng Res. 1999;73(3):297–309.

7. Zhu QC, Liu XJ, Hao TX, Zeng MF, Shen JB, Zhang FS, et al. Modeling soil acidification in typical Chinese cropping systems. Sci Total Environ. 2018;613:1339–48. doi: 10.1016/j.scitotenv.2017.06.257 28968946

8. Zeng XY, Ma YT, Ma LR. Utilization of straw in biomass energy in China. Renew Sust Energ Rev. 2007;11(5):976–87.

9. Chen JM, Li CL, Ristovski Z, Milic A, Gu YT, Islam MS, et al. A review of biomass burning: Emissions and impacts on air quality, health and climate in China. Sci Total Environ. 2017;579:1000–34. doi: 10.1016/j.scitotenv.2016.11.025 27908624

10. Sun JF, Peng HY, Chen JM, Wang XM, Wei M, Li WJ, et al. An estimation of CO2 emission via agricultural crop residue open field burning in China from 1996 to 2013. J Clean Prod. 2016;112:2625–31.

11. Qu CS, Li B, Wu HS, Giesy JP. Controlling Air Pollution from Straw Burning in China Calls for Efficient Recycling. Environ Sci Technol. 2012;46(15):7934–6. doi: 10.1021/es302666s 22822919

12. Biederman LA, Harpole WS. Biochar and its effects on plant productivity and nutrient cycling: a meta-analysis. Gcb Bioenergy. 2013;5(2):202–14.

13. Liu XY, Zhang AF, Ji CY, Joseph S, Bian RJ, Li LQ, et al. Biochar's effect on crop productivity and the dependence on experimental conditions-a meta-analysis of literature data. Plant Soil. 2013;373(1–2):583–94.

14. Anderson CR, Condron LM, Clough TJ, Fiers M, Stewart A, Hill RA, et al. Biochar induced soil microbial community change: Implications for biogeochemical cycling of carbon, nitrogen and phosphorus. Pedobiologia. 2011;54(5–6):309–20.

15. Abujabhah IS, Doyle RB, Bound SA, Bowman JP. Assessment of bacterial community composition, methanotrophic and nitrogen-cycling bacteria in three soils with different biochar application rates. J Soil Sediment. 2018;18(1):148–58.

16. Walters RD, White JG. Biochar In Situ Decreased Bulk Density and Improved Soil-Water Relations and Indicators in Southeastern US Coastal Plain Ultisols. Soil Sci. 2018;183(3):99–111.

17. Keech O, Carcaillet C, Nilsson MC. Adsorption of allelopathic compounds by wood-derived charcoal: the role of wood porosity. Plant Soil. 2005;272(1–2):291–300.

18. Lehmann J, Rillig MC, Thies J, Masiello CA, Hockaday WC, Crowley D. Biochar effects on soil biota—A review. Soil Biol Biochem. 2011;43(9):1812–36.

19. Yan S, Niu ZY, Zhang AG, Yan HT, Zhang H, He KX, et al. Biochar application on paddy and purple soils in southern China: soil carbon and biotic activity. Royal Society Open Science. 2019;6(7).

20. Kookana RS, Sarmah AK, Van Zwieten L, Krull E, Singh B. Biochar Application to Soil: Agronomic and Environmental Benefits and Unintended Consequences. Adv Agron. 2011;112:103–43.

21. Laird DA. The charcoal vision: A win-win-win scenario for simultaneously producing bioenergy, permanently sequestering carbon, while improving soil and water quality. Agron J. 2008;100(1):178–81.

22. Qi YC, Guo HX, Li K, Liu WQ. Comprehensive analysis of differential genes and miRNA profiles for discovery of topping-responsive genes in flue-cured tobacco roots. Febs J. 2012;279(6):1054–70. doi: 10.1111/j.1742-4658.2012.08497.x 22251798

23. Tang S, Wang Y, Li ZF, Gui YJ, Xiao BG, Xie JH, et al. Identification of wounding and topping responsive small RNAs in tobacco (Nicotiana tabacum). Bmc Plant Biol. 2012;12.

24. Weeks WW, Seltmann H. Effect of Sucker Control on the Volatile Compounds in Flue-Cured Tobacco. J Agr Food Chem. 1986;34(5):899–904.

25. Guo HX, Kan YC, Liu WQ. Differential Expression of miRNAs in Response to Topping in Flue-Cured Tobacco (Nicotiana tabacum) Roots. Plos One. 2011;6(12).

26. Yan S, Niu ZY, Yan HT, Yun F, Peng GX, Yang YF, et al. Biochar application significantly affects the N pool and microbial community structure in purple and paddy soils. Peerj. 2019;7.

27. Kumar S, Nakajima T, Mbonimpa EG, Gautam S, Somireddy UR, Kadono A, et al. Long-term tillage and drainage influences on soil organic carbon dynamics, aggregate stability and corn yield. Soil Sci Plant Nutr. 2014;60(1):108–18.

28. Agafonova NV, Doronina NV, Kaparullina EN, Fedorov DN, Gafarov AB, Sazonova OI, et al. A novel Delftia plant symbiont capable of autotrophic methylotrophy. Microbiology+. 2017;86(1):96–105.

29. Singh SK, Wu YM, Ghosh JS, Pattanaik S, Fisher C, Wang Y, et al. RNA-sequencing Reveals Global Transcriptomic Changes in Nicotiana tabacum Responding to Topping and Treatment of Axillary-shoot Control Chemicals. Sci Rep-Uk. 2015;5.

30. Li W, Zhang HL, Li XX, Zhang FX, Liu C, Du YM, et al. Intergrative metabolomic and transcriptomic analyses unveil nutrient remobilization events in leaf senescence of tobacco. Sci Rep-Uk. 2017;7.

31. Lohman BK, Weber JN, Bolnick DI. Evaluation of TagSeq, a reliable low‐cost alternative for RNA seq. Mol Ecol Resour. 2016;16(6):1315–21. doi: 10.1111/1755-0998.12529 27037501

32. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7(3):562–78. doi: 10.1038/nprot.2012.016 22383036

33. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–U130. doi: 10.1038/nbt.1883 21572440

34. Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. Bmc Bioinformatics. 2011;12.

35. Deng CL, Wang NN, Li SF, Dong TY, Zhao XP, Wang SJ, et al. Isolation of differentially expressed sex genes in garden asparagus using suppression subtractive hybridization. J Plant Res. 2015;128(5):829–38. doi: 10.1007/s10265-015-0735-6 26038270

36. Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010;11(2).

37. Zhou Q, Guo JJ, He CT, Shen C, Huang YY, Chen JX, et al. Comparative Transcriptome Analysis between Low- and High-Cadmium-Accumulating Genotypes of Pakchoi (Brassica chinensis L.) in Response to Cadmium Stress. Environ Sci Technol. 2016;50(12):6485–94. doi: 10.1021/acs.est.5b06326 27228483

38. Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. Bmc Bioinformatics. 2008;9.

39. Mizusaki S, Noguchi M, Tamaki E. Studies on nitrogen metabolism in tobacco plants: VI. Metabolism of glutamic acid, γ-aminobutyric acid, and proline in tobacco leaves. Archives of Biochemistry and Biophysics. 1964;105(3):599–605.

40. Zhao JY, Li LL, Zhao YN, Zhao CX, Chen X, Liu PP, et al. Metabolic changes in primary, secondary, and lipid metabolism in tobacco leaf in response to topping. Anal Bioanal Chem. 2018;410(3):839–51. doi: 10.1007/s00216-017-0596-z 28929184

41. Zhang JX, Zhang ZF, Shen GM, Wang R, Gao L, Kong FY, et al. Growth Performance, Nutrient Absorption of Tobacco and Soil Fertility after Straw Biochar Application. Int J Agric Biol. 2016;18(5):983–9.

42. Wang J, Feng X, Cheng Q, Lian W, Yang S, Zhang J, et al. Effects of biochar application rate on chemical composition and neutral aroma constituent of tobacco leaf. Acta Agriculturae Jiangxi. 2016;28(3):16–9.

43. You CH, Jiang LF, Xi FH, Wang WW, Li MJ, Xu ZB, et al. Comparative Evaluation of Different Types of Soil Conditioners with Respect to Their Ability to Remediate Consecutive Tobacco Monoculture Soil. Int J Agric Biol. 2015;17(5):969–75.

44. Mitsui K, David F, Dumont E, Ochiai N, Tamura H, Sandra P. LC fractionation followed by pyrolysis GC-MS for the in-depth study of aroma compounds formed during tobacco combustion. J Anal Appl Pyrol. 2015;116:68–74.

45. Grunwald C, Sims J, Sheen S. Effects of nitrogen fertilization and stalk position on chlorophyll, carotenoids, and certain lipids of three tobacco genotypes. Canadian Journal of Plant Science. 1977;57(2):525–35.


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2019 Číslo 10