About this Journal Submit a Manuscript Table of Contents
Archaea
Volume 2013 (2013), Article ID 870825, 12 pages
http://dx.doi.org/10.1155/2013/870825
Research Article

Archaeal Assemblages Inhabiting Temperate Mixed Forest Soil Fluctuate in Taxon Composition and Spatial Distribution over Time

Biology Department, University of Northern Iowa, MSH 17, Cedar Falls, IA 50614, USA

Received 19 April 2013; Revised 26 June 2013; Accepted 29 June 2013

Academic Editor: William B. Whitman

Copyright © 2013 Colby A. Swanson and Marek K. Sliwinski. 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. S. Timonen and M. Bomberg, “Archaea in dry soil environments,” Phytochemistry Reviews, vol. 8, no. 3, pp. 505–518, 2009. View at Publisher · View at Google Scholar · View at Scopus
  2. C. Brochier-Armanet, B. Boussau, S. Gribaldo, and P. Forterre, “Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota,” Nature Reviews Microbiology, vol. 6, no. 3, pp. 245–252, 2008. View at Publisher · View at Google Scholar · View at Scopus
  3. A. Spang, R. Hatzenpichler, C. Brochier-Armanet et al., “Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota,” Trends in Microbiology, vol. 18, no. 8, pp. 331–340, 2010. View at Publisher · View at Google Scholar · View at Scopus
  4. S. Leininger, T. Urich, M. Schloter et al., “Archaea predominate among ammonia-oxidizing prokaryotes in soils,” Nature, vol. 442, no. 7104, pp. 806–809, 2006. View at Publisher · View at Google Scholar · View at Scopus
  5. M. Könneke, A. E. Bernhard, J. R. De La Torre, C. B. Walker, J. B. Waterbury, and D. A. Stahl, “Isolation of an autotrophic ammonia-oxidizing marine archaeon,” Nature, vol. 437, no. 7058, pp. 543–546, 2005. View at Publisher · View at Google Scholar · View at Scopus
  6. J. R. De La Torre, C. B. Walker, A. E. Ingalls, M. Könneke, and D. A. Stahl, “Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol,” Environmental Microbiology, vol. 10, no. 3, pp. 810–818, 2008. View at Publisher · View at Google Scholar · View at Scopus
  7. R. Hatzenpichler, E. V. Lebedeva, E. Spieck et al., “A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 6, pp. 2134–2139, 2008. View at Publisher · View at Google Scholar · View at Scopus
  8. M. Tourna, M. Stieglmeier, A. Spang et al., “Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 20, pp. 8420–8425, 2011. View at Publisher · View at Google Scholar · View at Scopus
  9. L. E. Lehtovirta-Morley, K. Stoecker, A. Vilcinskas, J. I. Prosser, and G. W. Nicol, “Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 38, pp. 15892–15897, 2011. View at Publisher · View at Google Scholar · View at Scopus
  10. M.-Y. Jung, S.-J. Park, D. Min et al., “Enrichment and characterization of an autotrophic ammonia-oxidizing archaeon of mesophilic crenarchaeal group I.1a from an agricultural soil,” Applied and Environmental Microbiology, vol. 77, no. 24, pp. 8635–8647, 2011. View at Publisher · View at Google Scholar · View at Scopus
  11. J.-G. Kim, M.-Y. Jung, S.-J. Park et al., “Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil,” Environmental Microbiology, vol. 14, pp. 1528–1543, 2012. View at Publisher · View at Google Scholar · View at Scopus
  12. H. M. Simon, C. E. Jahn, L. T. Bergerud et al., “Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots,” Applied and Environmental Microbiology, vol. 71, no. 8, pp. 4751–4760, 2005. View at Publisher · View at Google Scholar · View at Scopus
  13. A. Spang, A. Poehlein, P. Offre, S. Zumbraegel, S. Haider, N. Rychlik, et al., “The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations,” Environmental Microbiology, vol. 14, no. 12, pp. 3122–3145, 2012. View at Publisher · View at Google Scholar
  14. S. B. Bintrim, T. J. Donohue, J. Handelsman, G. P. Roberts, and R. M. Goodman, “Molecular phylogeny of Archaea from soil,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 1, pp. 277–282, 1997. View at Publisher · View at Google Scholar · View at Scopus
  15. C. H. Ettema and D. A. Wardle, “Spatial soil ecology,” Trends in Ecology and Evolution, vol. 17, no. 4, pp. 177–183, 2002. View at Publisher · View at Google Scholar · View at Scopus
  16. G. L. Grundmann and D. Debouzie, “Geostatistical analysis of the distribution of NH4+ and NO2--oxidizing bacteria and serotypes at the millimeter scale along a soil transect,” FEMS Microbiology Ecology, vol. 34, no. 1, pp. 57–62, 2000. View at Publisher · View at Google Scholar · View at Scopus
  17. S. T. Bates, D. Berg-Lyons, J. G. Caporaso, W. A. Walters, R. Knight, and N. Fierer, “Examining the global distribution of dominant archaeal populations in soil,” ISME Journal, vol. 5, no. 5, pp. 908–917, 2011. View at Publisher · View at Google Scholar · View at Scopus
  18. M. K. Sliwinski and R. M. Goodman, “Spatial heterogeneity of crenarchaeal assemblages within mesophilic soil ecosystems as revealed by PCR-single-stranded conformation polymorphism profiling,” Applied and Environmental Microbiology, vol. 70, no. 3, pp. 1811–1820, 2004. View at Publisher · View at Google Scholar · View at Scopus
  19. M. K. Sliwinski and R. M. Goodman, “Comparison of crenarchaeal consortia inhabiting the rhizosphere of diverse terrestrial plants with those in bulk soil in native environments,” Applied and Environmental Microbiology, vol. 70, no. 3, pp. 1821–1826, 2004. View at Publisher · View at Google Scholar · View at Scopus
  20. C. A. Schneider, W. S. Rasband, and K. W. Eliceiri, “NIH Image to ImageJ: 25 years of image analysis,” Nature Methods, vol. 9, pp. 671–675, 2012. View at Publisher · View at Google Scholar
  21. T. Z. DeSantis, P. Hugenholtz, N. Larsen et al., “Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB,” Applied and Environmental Microbiology, vol. 72, no. 7, pp. 5069–5072, 2006. View at Publisher · View at Google Scholar · View at Scopus
  22. P. D. Schloss, S. L. Westcott, T. Ryabin et al., “Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities,” Applied and Environmental Microbiology, vol. 75, no. 23, pp. 7537–7541, 2009. View at Publisher · View at Google Scholar · View at Scopus
  23. P. D. Schloss, “Evaluating different approaches that test whether microbial communities have the same structure,” ISME Journal, vol. 2, no. 3, pp. 265–275, 2008. View at Publisher · View at Google Scholar · View at Scopus
  24. S. Guindon, J.-F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, and O. Gascuel, “New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0,” Systematic Biology, vol. 59, no. 3, pp. 307–321, 2010. View at Publisher · View at Google Scholar · View at Scopus
  25. D. Darriba, G. L. Taboada, R. Doallo, and D. Posada, “jModelTest 2: more models, new heuristics and parallel computing,” Nature Methods, vol. 9, pp. 772–772, 2012.
  26. D. McDonald, M. N. Price, J. Goodrich et al., “An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea,” ISME Journal, vol. 6, no. 3, pp. 610–618, 2012. View at Publisher · View at Google Scholar · View at Scopus
  27. J.-C. Auguet, A. Barberan, and E. O. Casamayor, “Global ecological patterns in uncultured Archaea,” ISME Journal, vol. 4, no. 2, pp. 182–190, 2010. View at Publisher · View at Google Scholar · View at Scopus