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MOLECULAR-BASED APPROACHES TO SOIL MICROBIOLOGY

Fluorescent In Situ Hybridization and Micro-autoradiography Applied to Ecophysiology in Soil

^a U.S. Environmental Protection Agency, National Risk Management Research Lab., 26 W. Martin Luther King Dr., MS 421, Cincinnati, OH 45268
^b USDA-ARS, National Soil Tilth Lab., 2150 Pammel Dr., Ames, IA 50011
^c Dep. of Civil, Construction, and Environ. Eng., 486 Town Engineering Bldg., Iowa State Univ., Ames, IA 50011

^* Corresponding author (rogers.shane{at}epa.gov).

Soil microbial communities perform many important processes, including nutrient cycling, plant–microorganism interactions, and degradation of xenobiotics. The study of microbial communities, however, has been limited by cultural methods, which may greatly underestimate diversity. The advent of nucleic acids technologies allows microbial communities to be quantified and classified without the limitations of cultivation. Fluorescent in situ hybridization (FISH) and other tools of molecular ecology are now being used to investigate community structure and diversity of soils, aquifers, and other natural habitats. Based on these studies, soil microbial communities are diverse and appear to respond to anthropogenic inputs, such as fertilizer, manure, and pollutants, as well as the more well-known constraints imposed by temperature and moisture. Yet most nucleic-acids-based technologies are unable to directly link phylogeny with processes in a manner similar to cultivation-based approaches, restricting the conclusions that can be drawn from the large data sets they generate. Recently, the combination of FISH with microautoradiography (FISH-MAR) allows cells active in processes to be quantified and simultaneously classified phylogenetically. In this review, we discuss how FISH-MAR can be used to quantify the specific microbial phylotype(s) responsible for a microbially catalyzed process. Examples of the use of FISH and FISH-MAR in soils and sediments are described. The capabilities and limitations of these techniques for linking microbial community structure and function are discussed.

Abbreviations: CLSM, confocal laser scanning microscopy • FISH, fluorescent in situ hybridization • MAR, microautoradiography • PCR, polymerase chain reaction.