Ecological Archives E088-084-A3

Noah Fierer, Mark A. Bradford, and Robert B. Jackson. 2007. Towards an ecological classification of soil bacteria. Ecology 88:1354–1364.

Appendix C. References for the clone library meta-analysis (Fig. 3).

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Borneman, J., P. W. Skroch, K. M. O’ Sullivan, J. A. Palus, N. G. Rumjanek, J. L. Jansen, J. Nienhuis, and E. W. Triplett. 1996. Molecular microbial diversity of an agricultural soil in Wisconsin. Applied and Environmental Microbiology 62:1935–1943.

Chelius, M. K., and E. W. Triplett. 2001. The diversity of archaea and bacteria in association with the roots of Zea mays L. Microbial Ecology 41:252–263.

Chow, M. L., C. C. Radomski, J. M. McDermott, J. Davies, and P. E. Axelrood. 2002. Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source. FEMS Microbiology Ecology 42:347–357.

Furlong, M. A., D. R. Singleton, D. C. Coleman, and W. B. Whitman. 2002. Molecular and culture-based analyses of prokaryotic communities from an agricultural soil and the burrows and casts of the earthworm Lumbricus rubellus. Applied and Environmental Microbiology 68:1265–1279.

Gremion, F., A. Chatzinotas, and H. Harms. 2003. Comparative 16S rDNA and 16S rRNA sequence analysis indicates that Actinobacteria might be a dominant part of the metabolically active bacteria in heavy metal-contaminated bulk and rhizosphere soil. Environmental Microbiology 5:896–907.

Hery, M., A. Herrera, T. M. Vogel, P. Normand, and E. Navarro. 2005. Effect of carbon and nitrogen input on the bacterial community structure of Neocaledonian nickel mine spoils. FEMS Microbiology Ecology 51:333–340.

Kaiser, O., A. Puhler, and W. Selbitschka. 2001. Phylogenetic analysis of microbial diversity in the rhizoplane of oilseed rape (Brassica napus cv. Westar) employing cultivation-dependent and cultivation-independent approaches. Microbial Ecology 42:136–149.

Liesack, W., and E. Stackebrandt. 1992. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. Journal of Bacteriology 174:5072–5078.

Liles, M. R., B. F. Manske, S. B. Bintrim, J. Handelsman, and R. M. Goodman. 2003. A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Applied and Environmental Microbiology 69:2684–2691.

Lipson, D. A., and S. K. Schmidt. 2004. Seasonal changes in an alpine soil bacterial community in the Colorado Rocky Mountains. Applied and Environmental Microbiology 70:2867–2879.

Marilley, L., and M. Aragno. 1999. Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots. Applied Soil Ecology 13:127–136.

McCaig, A. E., L. A. Glover, and J. I. Prosser. 1999. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Applied and Environmental Microbiology 65:1721–1730.

Nogales, B., E. R. B. Moore, E. Llobet-Brossa, R. Rossello-Mora, R. Amann, and K. N. Timmis. 2001. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Applied and Environmental Microbiology 67:1874–1884.

Tringe, S., C. von Mering, A. Kobayashi, A. Salamov, K. Chen, H. Chang, M. Podar, J. Short, E. Mathur, J. Detter, P. Bork, P. Hugenholtz, and E. Rubin. 2005. Comparative metagenomics of microbial communities. Science 308:554–557.

Zhou, J. Z., B. C. Xia, H. S. Huang, D. S. Treves, L. J. Hauser, R. J. Mural, A. V. Palumbo, and J. M. Tiedje. 2003. Bacterial phylogenetic diversity and a novel candidate division of two humid region, sandy surface soils. Soil Biology and Biochemistry 35:915–924.

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