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MOLECULAR-BASED APPROACHES TO SOIL MICROBIOLOGY

Symposium: Molecular-Based Approaches to Soil Microbiology

^a Everglades Program Team, A.R.M. Loxahatchee National Wildlife Refuge, 10216 Lee Road, Boynton Beach, FL 33437-9741
^b Department of Biological Sciences, Florida International University, University Park, Miami, FL, 33199
^c Department of Environmental Studies, Florida International University, University Park, Miami, FL, 33199
^d USDA Agricultural Research Service, National Soil Tilth Laboratory, Agricultural Land and Watershed, Management Research, 2150 Pammel Drive, Ames, IA, 50011-3120

^*Corresponding author (James_Entry{at}nps.gov).

Microorganisms exhibit an impressive diversity in their metabolic activities and in their interactions with other microbes, plants, and animals. It is because of this intrinsic structural and functional diversity of microbial communities that, in the past, it has been nearly impossible to discern underlying patterns within natural and agricultural ecosystems. As a result, in the discussion of ecosystem processes, soil microbes are often placed in a ‘black box’, inputs and outputs measured, but most of the processes that go on inside ‘the box’ are based on inference. Recently, there has been an explosion in the identification of microorganisms in the natural world using culture-independent techniques. Nucleic acid analyses of the whole microbial community provide higher resolution and help answer questions that have not been possible with standard microbiological cultured-based methods. The 16S and 18S regions of the ribosomal small subunit genes sequences have become the universal phylogenetic markers for the study of microbial systematics and ecological surveys from the natural environments. Ribosomal molecules have highly conserved sequence domains interspersed with hypervariable regions and it is these variable domains that can distinguish one microbe from another and therefore, can be used as molecular markers to discriminate among taxa.

Molecular tools allow us to measure the soil microbial community and with higher resolution than culture based approaches. Advances in soil microbiology will be intimately linked with molecular biological tools. The Molecular-Based Approaches to Soil Microbiology symposium focused on molecular approach of soil microbiology from community analysis to stable isotope analysis. Review articles will describe molecular methods used to investigate soil microbial communities such as density gradient gel electrophoresis (DGGE), length heterogeneity-PCR (LH-PCR), terminal restriction fragment length polymorphism (TRFLP) and clone libraries and sequences. Other articles review the use of fluorescence in situ hybridization (FISH), stable isotope probing and molecular analysis of ectomycorrhizal communities to identify and track specific soil microorganisms. This collection of reviews will educate and encourage soil scientists to use molecular-based research approaches and keep our society on the cutting edge of soil science.

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Received for publication December 6, 2006.

This Article Full Text (PDF) Free Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Entry, J. A. Articles by Moorman, T. B. Search for Related Content PubMed Articles by Entry, J. A. Articles by Moorman, T. B. Agricola Articles by Entry, J. A. Articles by Moorman, T. B.