Chapter 47 : Introduction and Overview: Soil, Rhizosphere, and Phyllosphere

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To the uninitiated, it might seem almost paradoxical that such an outwardly humble substance as soil should bear such advanced technical treatments as those presented here: microarrays, reporter genes, molecular probes, fluorescence microscopy, metagenomics, proteomics, and others. However, soil microbial communities are arguably among the most complex biological entities, dwelling in extremely heterogeneous and complex physical environments. The study of plant-associated microbial communities presents challenges similar to those encountered in soils. Environmental microbiology is a dynamic field that has produced many innovations in recent decades. A section presents both classical and cutting-edge techniques in an attempt to summarize the current state of the field.

Citation: Lipson D. 2007. Introduction and Overview: Soil, Rhizosphere, and Phyllosphere, p 595-596. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch47

Key Concept Ranking

Horizontal Gene Transfer
Soil Microbial Communities
Environmental Microbiology
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1. Andrews, J. H.,, and R. F. Harris. 2000. The ecology and biogeography of microorganisms of plant surfaces. Annu. Rev. Phytopathol. 38:145180.
2. Bode, H. B.,, B. Bethe,, R. Hofs, and, A. Zeeck. 2002. Big effects from small changes: possible ways to explore nature’s chemical diversity. Chembiochem 3:619627.
3. Burns, R. G.,, and J. E. M. Stach. 2002. Microbial ecology of soil biofilms: substrate bioavailability, bioremediation and complexity. Dev. Soil Sci. 28B:1742.
4. Canadell, J.,, R. B. Jackson,, J. R. Ehleringer,, H. A. Mooney,, O. E. Sala, and, E. D. Schulze. 1996. Maximum rooting depth of vegetation types at the global scale. Oecologia 108:583595.
5. Chatzinotas, A.,, R. A. Sandaa,, W. Shoenhuber,, R. Amann,, F. L. Daae,, V. Torsvik,, J. Zeyer, and, D. Hahn. 1998. Analysis of broad-scale differences in microbial community composition of two pristine forest soils. Syst. Appl. Microbiol. 21:579587.
6. Chin, K.-J.,, D. Hahn,, U. Hengstmann,, W. Liesack, and, P. H. Janssen. 1999. Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms. Appl. Environ. Microbiol. 65:50425049.
7. Curtis, T. P.,, W. T. Sloan, and, J. W. Scannall. 2002. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA 99:1049410499.
8. Fierer, N.,, and R. B. Jackson. 2006. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA 103:626631.
9. Hinsinger, P.,, G. R. Gobran,, P. J. Gregory, and, W. W. Wenzel. 2005. Rhizosphere geometry and heterogeneity arising from root-mediated physical and chemical processes. New Phytol. 168:293303.
10. Horner-Devine, M. C.,, M. Lage,, J. B. Hughes, and, B. J. M. Bohannan. 2004. A taxa-area relationship for bacteria. Nature 432:750753.
11. Hughes Martiny, J. B.,, B. J. M. Bohannan,, J. H. Brown,, R. K. Colwell,, J. A. Fuhrman,, J. L. Green,, M. C. Horner-Devine,, M. Kane,, J. Adams-Krumins,, C. R. Kuske,, P. J. Morin,, S. Naeem,, L. Øvreås,, A.-L. Reysenbach,, V. H. Smith, and, J. T. Staley. 2006. Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 4:102112.
12. Joseph, S. J.,, P. Hugenholtz,, P. Sangwan,, C. A. Osborne, and, P. H. Janssen. 2003. Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl. Environ. Microbiol. 69:72107215.
13. Lindow, S. E.,, and M. T. Brandl. 2003. Microbiology of the phyllosphere. Appl. Environ. Microbiol. 69:18751883.
14. Lipson, D. A.,, M. Blair,, K. Grieve,, G. Barron-Gafford, and, R. Murthy. 2006. Relationships between microbial community structure and soil processes under elevated atmospheric carbon dioxide. Microb. Ecol. 51:302314.
15. Manefield, M. W.,, A. S. Whiteley,, R. I. Griffiths, and, M. J. Bailey. 2002. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl. Environ. Microbiol. 68:53675373.
16. Molin, S.,, and T. Tolker-Nielsen. 2003. Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure. Curr. Opin. Biotechnol. 14:255261.
17. Morris, C. E.,, and J. M. Monier. 2003. The ecological significance of biofilm formation by plant-associated bacteria. Annu. Rev. Phytopathol. 41:429453.
18. Radajewski, S.,, P. Ineson,, N. R. Parekh, and, J. C. Murrell. 2000. Stable-isotope probing as a tool in microbial ecology. Nature 403:646649.
19. Ritz, K.,, B. S. Griffiths,, V. L. Torsvik, and, N. B. Hendriksen. 1997. Analysis of soil and bacterioplankton community DNA by melting profiles and reassociation kinetics. FEMS Microbiol. Lett. 149:151156.
20. Saleh-Lakha, S.,, M. Miller,, R. G. Campbell,, K. Schneider,, P. Elahimanesh,, M. M. Hart, and, J. T. Trevors. 2005. Microbial gene expression in soil: methods, applications and challenges. J. Microbiol. Methods 63:119.
21. Schenk, H. J.,, and R. B. Jackson. 2005. Mapping the global distribution of deep roots in relation to climate and soil characteristics. Geoderma 126:129140.
22. Schulten, H.-R.,, and M. Schnitzer. 1998. The chemistry of soil organic nitrogen: a review. Biol. Fertil. Soils 26:115.
23. Torsvik, V.,, and L. Øvreås. 2002. Microbial diversity and function in soil: from genes to ecosystems. Curr. Opin. Microbiol. 5:240245.

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