The bacteria and archaea in soil

Modern Soil Microbiology, Second Edition

Volumn , Issue , 2006, Pages 83-106

  Van Elsas, Jan Dirk ^a   Torsvik, Vigdis ^b   Hartmann, Anton ^c   Øvreås, Lise ^b   Jansson, Janet K ^d  

^a UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

^b UNIVERSITY OF BERGEN   (Norway)

^c INSTITUTE OF EPIDEMIOLOGY   (Germany)

^d SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85057421370     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (32)

1. Gans, J., Wolinsky, M., and Dunbar, J., Computational improvements reveal great bacterial diversity and high metal toxicity in soil, Science, 309, 1387-1390, 2005.
2. Bottomley, P. J., Light microscopic methods for studying soil microorganisms, In Methods of Soil Analysis, Part 2, Weaver, R. W., Angle, S., Bottomley, P., Bezdicek, D., Smith, S., Tabatabai, A., Wollum, A., Mickelson, S. H., and Bingham, J. M., Eds., Soil Science Society of America, Madison, WI, pp. 81-105, 1994.
3. Stenström, J., Stenberg, B., and Johansson, M., Kinetics of substrate-induced respiration (SIR): Theory, AMBIO, 27, 35-39, 1998.
4. Stenström, J., Svensson, K., and Johansson, M., Reversible transition between active and dormant microbial states in soil, FEMS Microbiology Ecology, 36, 93-104, 2001.
5. Ludwig, W., Bauer, S. H., Bauer, M., Held, I., Kirchhof, G., Schulze, R., Huber, I., Spring, S., Hartmann, A., and Schleifer, K. H., Detection and in situ localization of representatives of a widely distributed new bacterial phylum, FEMS Microbiology Letters, 153, 181-190, 1997.
6. Sait, M., Hugenholtz, P., and Janssen, P. H., Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation- independent surveys, Environmental Microbiology, 4, 654-666, 2002.
7. Zengler, K., Toledo, G., Rappe, M., Elkins, J., Mathur, E. J., Short, J. M., and Keller, M., Cultivating the uncultured, PNAS, 99, 15681-15686, 2002.
8. Bruns, A., Cypionka, H., and Overmann, J., Cyclic AMP and Acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic sea, Applied and Environmental Microbiology, 68, 3978-3987, 2002.
9. George, Garrity, Ed, Bergey’s Manual of Systematic Bacteriology 2nd ed., Springer Verlag, Berlin, 2005.
10. Seldin, L., Rosado, A. S., da Cruz, D. W., Nobrega, A., van Elsas, J. D., and Paiva, E., Comparison of Paenibacillus azotofixans strains isolated from rhizoplane, rhizosphere, and non-root-associated soil from maize planted in two different brazilian soils, Applied and Environmental Microbiology, 64, 3860-3868, 1998.
11. Jensen, G. B., Hansen, B. M., Eilenberg, J., and Mahillon, J., The hidden lifestyles of Bacillus cereus and relatives, Environmental Microbiology, 5, 631, 2003.
12. Bertaux, J., Schmid, M., Prevost-Boure, N. C., Churin, J. L., Hartmann, A., Garbaye, J., and Frey-Klett, P., In situ identification of intracellular bacteria related to Paenibacillus spp. in the mycelium of the ectomycorrhizal fungus Laccaria bicolor S238N, Applied and Environmental Microbiology, 69, 4243-4248, 2003.
13. Quesada-Moraga, E., Garcia-Tovar, E., Valverde-Garcia, P., and Santiago-Alvarez, C., Isolation, geographical diversity and insecticidal activity of Bacillus thuringiensis from soils in Spain, Microbiological Research, 159, 59-71, 2004.
14. Mock, M. and Fouet, A., Anthrax, Annual Review of Microbiology, 55, 647-671, 2001.
15. Gust, B., Challis, G. L., Fowler, K., Kieserm, T., and Chater, K. F., PCRtargeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin, PNAS, 100, 1541-1546, 2003.
16. Buckley, D. H. and Schmidt, T. M., Diversity and dynamics of microbial communities in soils from agro-ecosystems, Environmental Microbiology, 5, 441-452, 2003.
17. Hugenholtz, P., Goebel, B., and Pace, N., Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity, Journal of Bacteriology, 180, 4765-4774, 1998.
18. DeLong, E., Microbial population genomics and ecology, Current Opinion in Microbiology, 5, 520-524, 2002.
19. DeLong, E., Microbial population genomics and ecology: The road ahead, Environmental Microbiology, 6, 875-878, 2004.
20. Dojka, M. A., Harris, J. K., and Pace, N. R., Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria, Applied and Environmental Microbiology, 66, 1617-1621, 2000.
21. Hugenholtz, P., Tyson, G., Webb, R., Wagner, A., and Blackall, L., Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives, Applied and Environmental Microbiology, 67, 411-419, 2001.
22. Joseph, S. J., Hugenholtz, P., Sangwan, P., Osborne, C. A., and Janssen, P. H., Laboratory cultivation of widespread and previously uncultured soil bacteria, Applied and Environmental Microbiology., 69, 7210-7215, 2003.
23. Janssen, P. H., Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes, Applied and Environmental Microbiology, 72, 1719-1728, 2006.
24. Schleper, C., Jurgens, G., and Jonuscheit, M., Genomic studies of uncultivated archaea, Nature Reviews Microbiology, 3, 479-488, 2005.
25. Simon, H. M., Dodsworth, J. A., and Goodman, R. M., Crenarchaeota colonize terrestrial plant roots, Environmental Microbiology, 2, 495-505, 2000.
26. Sliwinski, M. K. and Goodman, R. M., Comparison of crenarchaeal consortia inhabiting the rhizosphere of diverse terrestrial plants with those in bulk soil in native environments, Applied and Environmental Microbiology, 70, 1821-1826, 2004.
27. Pesaro, M. and Widmer, F., Identification of novel Crenarchaeota and Euryarchaeota clusters associated with different depth layers of a forest soil, FEMS Microbiology Ecology, 42, 89-98, 2002.
28. Wise, M. G., McArthur, J. V., and Shimkets, L. J., Methanotroph diversity in landfill soil: isolation of novel type I and type II methanotrophs whose presence was suggested by culture-independent 16S ribosomal DNA analysis, Applied and Environmental Microbiology, 65, 4887-4897, 1999.
29. Friedrich, M. W., Schmitt-Wagner, D., Lueders, T., and Brune, A., Axial differences in community structure of Crenarchaeota and Euryarchaeota in the highly compartmentalized gut of the soil-feeding termite Cubitermes orthognathus, Applied and Environmental Microbiology, 67, 4880-4890, 2001.
30. Rondon, M. R., August, P. R., Bettermann, A. D., Brady, S. F., Grossman, T. H., Liles, M. R., Loiacono, K. A. et al., Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms, Applied and Environmental Microbiology, 66, 2541-2547, 2000.
31. Tringe, S. G., von Mering, Christian, Kobayashi, Arthur, Salamov, Asaf A., Chen, Kevin, Chang, Hwai W., Podar, Mircea et al., Comparative Metagenomics of Microbial Communities, Science, 308, 554-557, 2005.
32. Van Overbeek, L. S., Eberl, L., Givskov, M., Molin, S., and van Elsas, J. D., Survival of, and induced stress resistance in, carbon-starved Pseudomonas fluorescens cells residing in soil, Applied and Environmental Microbiology, 61, 4202-4208, 1995.