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BioMed Research International
Volume 2015, Article ID 972481, 8 pages
http://dx.doi.org/10.1155/2015/972481
Research Article

Pyrosequencing Reveals Fungal Communities in the Rhizosphere of Xinjiang Jujube

1College of Forest, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong 271018, China
2College of Life Science, Shandong Agricultural University, Taian, Shandong 271018, China
3Research Institute of Forest in Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China

Received 18 September 2014; Revised 26 November 2014; Accepted 29 November 2014

Academic Editor: Ernesto Picardi

Copyright © 2015 Peng Liu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. T. Větrovský and P. Baldrian, “Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED,” Biology and Fertility of Soils, vol. 49, no. 8, pp. 1027–1037, 2013. View at Publisher · View at Google Scholar · View at Scopus
  2. M. W. Taylor, P. Tsai, N. Anfang, H. A. Ross, and M. R. Goddard, “Pyrosequencing reveals regional differences in fruit-associated fungal communities,” Environmental Microbiology, vol. 16, no. 9, pp. 2848–2858, 2014. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  3. S. J. Morris and G. P. Robertson, “Linking function between scales of resolution,” in The Fungal Community, J. Dighton, J. F. White, P. Oudemans, and J. F. White, Eds., pp. 13–26, Marcel Dekker, New York, NY, USA, 2005. View at Google Scholar
  4. J. L. Green, B. J. M. Bohannan, and R. J. Whitaker, “Microbial biogeography: from taxonomy to traits,” Science, vol. 320, no. 5879, pp. 1039–1043, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  5. J. Rousk, E. Baath, P. C. Brookes, C. L. Lauber, C. Lozupone, and J. G. Caporas, “Pesticide effects on bacterial diversity in agricultural soils-a review,” Microbial Ecology, vol. 33, pp. 443–453, 2001. View at Google Scholar
  6. P. Nannipieri, J. Ascher, M. T. Ceccherini, L. Landi, G. Pietramellara, and G. Renella, “Microbial diversity and soil functions,” European Journal of Soil Science, vol. 54, no. 4, pp. 655–670, 2003. View at Publisher · View at Google Scholar · View at Scopus
  7. S. M. D. Goldberg, J. Johnson, D. Busam et al., “A sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 30, pp. 11240–11245, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  8. R. Ohtonen, H. Fritze, T. Pennanen, A. Jumpponen, and J. Trappe, “Ecosystem properties and microbial community changes in primary succession on a glacier forefront,” Oecologia, vol. 119, no. 2, pp. 239–246, 1999. View at Publisher · View at Google Scholar · View at Scopus
  9. N. Fierer, D. Nemergut, R. Knight, and J. M. Craine, “Changes through time: integrating microorganisms into the study of succession,” Research in Microbiology, vol. 161, no. 8, pp. 635–642, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  10. E. R. Mardis, “The impact of next-generation sequencing technology on genetics,” Trends in Genetics, vol. 24, no. 3, pp. 133–141, 2008. View at Publisher · View at Google Scholar · View at PubMed
  11. R. Blaalid, T. Carlsen, S. Kumar et al., “Changes in the root-associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing,” Molecular Ecology, vol. 21, no. 8, pp. 1897–1908, 2012. View at Publisher · View at Google Scholar · View at Scopus
  12. A. Jumpponen and K. L. Jones, “Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere,” New Phytologist, vol. 184, no. 2, pp. 438–448, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  13. Y. W. Lim, B. K. Kim, C. Kim et al., “Assessment of soil fungal communities using pyrosequencing,” The Journal of Microbiology, vol. 48, no. 3, pp. 284–289, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  14. M. Buée, M. Reich, C. Murat et al., “454 pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity,” New Phytologist, vol. 184, no. 2, pp. 449–456, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  15. A. Jumpponen and K. L. Jones, “Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments,” New Phytologist, vol. 186, no. 2, pp. 496–513, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  16. M. Margulies, M. Egholm, W. E. Altman et al., “Genome sequencing in microfabricated high-density picolitre reactors,” Nature, vol. 437, pp. 376–380, 2005. View at Google Scholar
  17. Y. W. Lim, B. K. Kim, C. Kim et al., “Assessment of soil fungal communities using pyrosequencing,” Journal of Microbiology, vol. 48, no. 3, pp. 284–289, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  18. L. Tedersoo, R. H. Nilsson, K. Abarenkov et al., “454 pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases,” New Phytologist, vol. 188, no. 1, pp. 291–301, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  19. J. Wu, W. Liu, H. Zeng, L. Ma, and R. Bai, “Water quantity and quality of six lakes in the Arid Xingjiang Region, NW China,” Environmental Processes, vol. 1, no. 2, pp. 115–125, 2014. View at Publisher · View at Google Scholar
  20. W. Zhang, X. Long, X. Huo, Y. Chen, and K. Lou, “16S rRNA-based PCR-DGGE analysis of actinomycete communities in fields with continuous cotton cropping in Xinjiang, China,” Microbial Ecology, vol. 66, no. 2, pp. 385–393, 2013. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  21. L. Feng-gang, L. Wang, L. Yan-nan, L. Yang-yang, Z. Hai-yan, and Z. Li-li, “Analysis of culturable fungal diversity in ehizosphere soil of healthy and diseased cotton in Southern Xinjiang,” African Journal of Microbiology Research, vol. 6, pp. 7357–7364, 2012. View at Google Scholar
  22. J.-W. Li, L.-P. Fan, S.-D. Ding, and X.-L. Ding, “Nutritional composition of five cultivars of Chinese jujube,” Food Chemistry, vol. 103, no. 2, pp. 454–460, 2007. View at Publisher · View at Google Scholar · View at Scopus
  23. C. D. Moodie, H. W. Smith, and R. L. Hausanbuiler, Laboratory Manual for Soil Fertility, Washington State University Department of Agronomy Pullman, Washington, DC, USA, 1963.
  24. J. Zhao, R. Zhang, C. Xue et al., “Pyrosequencing reveals contrasting soil bacterial diversity and community structure of two main winter wheat cropping systems in China,” Microbial Ecology, vol. 67, no. 2, pp. 443–453, 2014. View at Publisher · View at Google Scholar · View at PubMed
  25. M. L. Jackson, Soil Chemical Analysis, Prentice Hall, Englewood Cliffs, NJ, USA, 1962.
  26. A. Walkey and I. A. Black, “An examination of the Degtjareff method for determining soil organic matter and a proposed modification of the chromic acid titration method,” Soil Science, vol. 37, no. 1, pp. 29–38, 1934. View at Publisher · View at Google Scholar
  27. O. O. Lee, Y. Wang, J. Yang, F. F. Lafi, A. Al-Suwailem, and P.-Y. Qian, “Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea,” The ISME Journal, vol. 5, no. 4, pp. 650–664, 2011. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  28. W. Jie, L. Lite, and D. Yang, “The correlation between freezing point and soluble solids of fruits,” Journal of Food Engineering, vol. 60, no. 4, pp. 481–484, 2003. View at Publisher · View at Google Scholar · View at Scopus
  29. J. Zhao, R. Zhang, C. Xue et al., “Pyrosequencing reveals contrasting soil bacterial diversity and community structure of two main winter wheat cropping systems in China,” Microbial Ecology, vol. 67, no. 2, pp. 443–453, 2014. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  30. M. Hu, X. Wang, X. Wen, and Y. Xia, “Microbial community structures in different wastewater treatment plants as revealed by 454-pyrosequencing analysis,” Bioresource Technology, vol. 117, pp. 72–79, 2012. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  31. Y.-X. Zeng, M. Yan, Y. Yu et al., “Diversity of bacteria in surface ice of Austre Lovénbreen glacier, Svalbard,” Archives of Microbiology, vol. 195, no. 5, pp. 313–322, 2013. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  32. J. A. Peiffer, A. Spor, O. Koren et al., “Diversity and heritability of the maize rhizosphere microbiome under field conditions,” Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 16, pp. 6548–6553, 2013. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  33. K. A. Seifert, “Integrating DNA barcoding into the mycological sciences,” Persoonia, vol. 21, pp. 162–166, 2008. View at Google Scholar
  34. M. Buée, M. Reich, C. Murat et al., “454 pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity,” New Phytologist, vol. 184, no. 2, pp. 449–456, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  35. L. F. W. Roesch, R. R. Fulthorpe, A. Riva et al., “Pyrosequencing enumerates and contrasts soil microbial diversity,” The ISME Journal, vol. 1, no. 4, pp. 283–290, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  36. L. N. Lemos, R. R. Fulthorpe, E. W. Triplett, and L. F. W. Roesch, “Rethinking microbial diversity analysis in the high throughput sequencing era,” Journal of Microbiological Methods, vol. 86, no. 1, pp. 42–51, 2011. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  37. C. W. Schadt, A. P. Martin, D. A. Lipson, and S. K. Schmidt, “Seasonal dynamics of previously unknown fungal lineages in tundra soils,” Science, vol. 301, no. 5638, pp. 1359–1361, 2003. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  38. H. E. O'Brien, J. L. Parrent, J. A. Jackson, J.-M. Moncalvo, and R. Vilgalys, “Fungal community analysis by large-scale sequencing of environmental samples,” Applied and Environmental Microbiology, vol. 71, no. 9, pp. 5544–5550, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  39. A. F. S. Taylor, “Fungal diversity in ectomycorrhizal communities: sampling effort and species detection,” Plant and Soil, vol. 244, no. 1-2, pp. 19–28, 2002. View at Publisher · View at Google Scholar · View at Scopus
  40. J. Rousk, E. Bååth, P. C. Brookes et al., “Soil bacterial and fungal communities across a pH gradient in an arable soil,” ISME Journal, vol. 4, no. 10, pp. 1340–1351, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  41. B. F. T. Brockett, C. E. Prescott, and S. J. Grayston, “Soil moisture is the major factor influencing microbial community structure and enzyme activities across seven biogeoclimatic zones in Western Canada,” Soil Biology and Biochemistry, vol. 44, no. 1, pp. 9–20, 2012. View at Publisher · View at Google Scholar · View at Scopus
  42. C. L. Lauber, M. S. Strickland, M. A. Bradford, and N. Fierer, “The influence of soil properties on the structure of bacterial and fungal communities across land-use types,” Soil Biology & Biochemistry, vol. 40, no. 9, pp. 2407–2415, 2008. View at Publisher · View at Google Scholar · View at Scopus
  43. J. Moukoumi, C. Munier-Lamy, J. Berthelin, and J. Ranger, “Effect of tree species substitution on organic matter biodegradability and mineral nutrient availability in a temperate topsoil,” Annals of Forest Science, vol. 63, no. 7, pp. 763–771, 2006. View at Publisher · View at Google Scholar · View at Scopus