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MOLECULAR-BASED APPROACHES TO SOIL MICROBIOLOGY

Assessing Microbial Community Diversity Using Amplicon Length Heterogeneity Polymerase Chain Reaction

^a Dep. of Biological Sci. and Intl. Forensic Research Inst., Florida International Univ., Miami, FL 33199
^b USDA-ARS, Northwest Irrigation and Soils Research Lab., Kimberly, ID 83341
^c Dep. of Environmental Science and Policy, George Mason Univ., Manassas, VA 20110.
^d Dep. of Biological Sci. and Intl. Forensic Research Inst., Florida International Univ., Miami, FL 33199

^* Corresponding author (millsd{at}fiu.edu).

It is thought that a microbial community is an assemblage of organisms, genes, and gene functions. Transient, acute signals such as excessive nutrient loads or disturbance and chronic signals such as seasonal temperature or rainfall impact the total environmental system. The goal of many microbial ecologists is to determine if a finely resolved study of microbial dynamics can be used as a large-scale biosensor to follow diversity patterns in the environment. With the development of new genomic tools, community-level studies have been designed that can interrogate the finer details of the biological components of a given habitat. Amplicon length heterogeneity polymerase chain reaction (LH-PCR) interrogates the hypervariable domains of the ribosomal small-subunit genes and separates these domains based on the naturally occurring sequence lengths of DNA. The amplicons are phylogenetically relevant in that the various amplicons generated can be directly associated with specific taxonomic sequences archived in the databases. The application of the LH-PCR technique as a monitoring tool for microbial ecology has been shown to enhance and extend the current understanding of the dynamics of microbial communities in their specific environments.

Abbreviations: bp, base pair • DGGE (TGGE) denaturing (or temperature) gradient gel electrophoresis • IGS, intergenic spacer • ITS, internally transcribed spacer • LH-PCR, length heterogeneity-polymerase chain reaction • rRNA, ribosomal ribonucleic acid • T-RFLP, terminal restriction length polymorphism • V1, V2, V3, variable domain 1, variable domain 2, variable domain 3 of the 16S ribosomal molecule.