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The Scientific World Journal
Volume 2014, Article ID 216071, 8 pages
http://dx.doi.org/10.1155/2014/216071
Research Article

Soil-Borne Microbial Functional Structure across Different Land Uses

1Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
2Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
3Department of Biology, Utrecht University, 3512 JE Utrecht, The Netherlands
4Institute of Biology, Leiden University, 2311 EZ Leiden, The Netherlands

Received 29 May 2014; Revised 26 June 2014; Accepted 16 July 2014; Published 10 August 2014

Academic Editor: Antonio Paz González

Copyright © 2014 Eiko E. Kuramae 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. J. I. Prosser, “Ecosystem processes and interactions in a morass of diversity,” FEMS Microbiology Ecology, vol. 81, no. 3, pp. 507–519, 2012. View at Publisher · View at Google Scholar · View at Scopus
  2. V. Torsvik and L. Øvreås, “Microbial diversity and function in soil: from genes to ecosystems,” Current Opinion in Microbiology, vol. 5, no. 3, pp. 240–245, 2002. View at Publisher · View at Google Scholar · View at Scopus
  3. E. A. Dinsdale, R. A. Edwards, D. Hall et al., “Functional metagenomic profiling of nine biomes,” Nature, vol. 452, no. 7214, pp. 629–632, 2008. View at Google Scholar · View at Scopus
  4. A. A. Navarrete, E. E. Kuramae, M. de Hollander, A. S. Pijl, J. A. van Veen, and S. M. Tsai, “Acidobacterial community responses to agricultural management of soybean in Amazon forest soils,” FEMS Microbiology Ecology, vol. 83, no. 3, pp. 607–621, 2013. View at Publisher · View at Google Scholar · View at Scopus
  5. G. A. Kowalchuk, B. Drigo, E. Yergeau, and J. A. van Veen, “Molecular approaches to assess the structure of bacterial and fungal communities in soil—the use of rRNA and other gene markers,” in Nucleic Acids and Proteins in Soil, P. Nannipieri and K. Smalla, Eds., pp. 159–188, Springer, Heidelberg, Germany, 2006. View at Google Scholar
  6. A. Priemé, G. Braker, and J. M. Tiedje, “Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils,” Applied and Environmental Microbiology, vol. 68, no. 4, pp. 1893–1900, 2002. View at Publisher · View at Google Scholar · View at Scopus
  7. G. Braker and J. M. Tiedje, “Nitric oxide reductase (norB) genes from pure cultures and environmental samples,” Applied and Environmental Microbiology, vol. 69, no. 6, pp. 3476–3483, 2003. View at Publisher · View at Google Scholar · View at Scopus
  8. T. Yan, M. W. Fields, L. Wu, Y. Zu, J. M. Tiedje, and J. Zhou, “Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater,” Environmental Microbiology, vol. 5, no. 1, pp. 13–24, 2003. View at Publisher · View at Google Scholar · View at Scopus
  9. X. D. Liu, S. M. Tiquia, G. Holguin et al., “Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico,” Applied and Environmental Microbiology, vol. 69, no. 6, pp. 3549–3560, 2003. View at Publisher · View at Google Scholar · View at Scopus
  10. S. W. Lee, J. Im, A. A. Dispirito, L. Bodrossy, M. J. Barcelona, and J. D. Semrau, “Effect of nutrient and selective inhibitor amendments on methane oxidation, nitrous oxide production, and key gene presence and expression in landfill cover soils: characterization of the role of methanotrophs, nitrifiers, and denitrifiers,” Applied Microbiology and Biotechnology, vol. 85, no. 2, pp. 389–403, 2009. View at Publisher · View at Google Scholar · View at Scopus
  11. L. Wu, L. Kellogg, A. H. Devol, J. M. Tiedje, and J. Zhou, “Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico,” Applied and Environmental Microbiology, vol. 74, no. 14, pp. 4516–4529, 2008. View at Publisher · View at Google Scholar · View at Scopus
  12. Z. He, Y. Deng, J. D. van Nostrand et al., “GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity,” ISME Journal, vol. 7, no. 9, pp. 1167–1179, 2010. View at Publisher · View at Google Scholar · View at Scopus
  13. J. R. Reeve, C. W. Schadt, L. Carpenter-Boggs, S. Kang, J. Zhou, and J. P. Reganold, “Effects of soil type and farm management on soil ecological functional genes and microbial activities,” ISME Journal, vol. 4, no. 9, pp. 1099–1107, 2010. View at Publisher · View at Google Scholar · View at Scopus
  14. E. M. H. Wellington, A. Berry, and M. Krsek, “Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing,” Current Opinion in Microbiology, vol. 6, no. 3, pp. 295–301, 2003. View at Publisher · View at Google Scholar · View at Scopus
  15. J. Zhou and D. K. Thompson, “Challenges in applying microarrays to environmental studies,” Current Opinion in Biotechnology, vol. 13, no. 3, pp. 204–207, 2002. View at Publisher · View at Google Scholar · View at Scopus
  16. V. J. Denef, J. Park, J. L. M. Rodrigues, T. V. Tsoi, S. A. Hashsham, and J. M. Tiedje, “Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities,” Environmental Microbiology, vol. 5, no. 10, pp. 933–943, 2003. View at Publisher · View at Google Scholar · View at Scopus
  17. E. E. Kuramae, E. Yergeau, L. C. Wong, A. S. Pijl, J. A. Van Veen, and G. A. Kowalchuk, “Soil characteristics more strongly influence soil bacterial communities than land-use type,” FEMS Microbiology Ecology, vol. 79, no. 1, pp. 12–24, 2012. View at Publisher · View at Google Scholar · View at Scopus
  18. Z. He, T. J. Gentry, C. W. Schadt et al., “GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes,” ISME Journal, vol. 1, no. 1, pp. 67–77, 2007. View at Publisher · View at Google Scholar · View at Scopus
  19. Y. Benjamini and Y. Hochberg, “Controlling the false discovery rate: a practical and powerful approach to multiple testing,” Journal of the Royal Statistical Society B: Methodological, vol. 57, no. 1, pp. 289–300, 1995. View at Google Scholar · View at MathSciNet
  20. C. J. F. ter Braak and P. Šmilauer, CANOCO Reference Manual and CanoDraw for Windows User's Guide: Software for Canonical Community Ordination (Version 4.5), Microcomputer Power, Ithaca, NY, USA, 2002.
  21. K. Killham, M. Amato, and J. N. Ladd, “Effect of substrate location in soil and soil pore-water regime on carbon turnover,” Soil Biology and Biochemistry, vol. 25, no. 1, pp. 57–62, 1993. View at Publisher · View at Google Scholar · View at Scopus
  22. S. Manzoni, R. B. Jackson, J. A. Trofymow, and A. Porporato, “The global stoichiometry of litter nitrogen mineralization,” Science, vol. 321, no. 5889, pp. 684–686, 2008. View at Publisher · View at Google Scholar · View at Scopus
  23. M. W. I. Schmidt, M. S. Torn, S. Abiven et al., “Persistence of soil organic matter as an ecosystem property,” Nature, vol. 478, no. 7367, pp. 49–56, 2011. View at Publisher · View at Google Scholar · View at Scopus
  24. X. H. Wu, T. D. Ge, H. Z. Yuan et al., “Changes in bacterial CO2 fixation with depth in agricultural soils,” Appiedl Microbiology Biotechnology, vol. 98, no. 5, pp. 2309–2319, 2014. View at Publisher · View at Google Scholar
  25. J. K. Edzwald, D. C. Toensing, and M. C. Leung, “Phosphate adsorption reactions with clay minerals,” Environmental Science and Technology, vol. 10, no. 5, pp. 485–490, 1976. View at Publisher · View at Google Scholar · View at Scopus
  26. J. Nikiema, R. Brzezinski, and M. Heitz, “Influence of phosphorus, potassium, and copper on methane biofiltration performance,” Canadian Journal of Civil Engineering, vol. 37, no. 2, pp. 335–345, 2010. View at Publisher · View at Google Scholar · View at Scopus
  27. H. L. T. Mobley and R. P. Hausinger, “Microbial ureases: significance, regulation, and molecular characterization,” Microbiological Reviews, vol. 53, no. 1, pp. 85–108, 1989. View at Google Scholar · View at Scopus
  28. H. L. T. Mobley, M. D. Island, and R. P. Hausinger, “Molecular biology of microbial ureases,” Microbiological Reviews, vol. 59, no. 3, pp. 451–480, 1995. View at Google Scholar · View at Scopus