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Volume 2013 (2013), Article ID 870825, 12 pages
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.
- S. Timonen and M. Bomberg, “Archaea in dry soil environments,” Phytochemistry Reviews, vol. 8, no. 3, pp. 505–518, 2009.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- C. H. Ettema and D. A. Wardle, “Spatial soil ecology,” Trends in Ecology and Evolution, vol. 17, no. 4, pp. 177–183, 2002.
- G. L. Grundmann and D. Debouzie, “Geostatistical analysis of the distribution of and -oxidizing bacteria and serotypes at the millimeter scale along a soil transect,” FEMS Microbiology Ecology, vol. 34, no. 1, pp. 57–62, 2000.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.