ARS | Publication request: Fluorescent In Situ Hybridization and Microautoradiography Applied to Ecophysiology in Soil

Submitted to: Soil Science Society of America Journal
Publication Type: Review Article
Publication Acceptance Date: September 23, 2006
Publication Date: March 30, 2007
Citation: Rogers, S.W., Moorman, T.B., Ong, S. 2007. Fluorescent In Situ Hybridization and Microautoradiography Applied to Ecophysiology in Soil. Soil Science Society of America Journal. 71:620-631.

Technical Abstract: Soil microbial communities perform many important processes,including nutrient cycling, plant-microorganism interactions, and degradation of xenobiotics. However, the study of microbial communities can be restricted by limitations imposed by cultural methods, which may greatly underestimate diversity. The advent of nucleic acids technologies has provided a means by which microbial communities can be studied 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 communities. 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 that can be detected through microautoradiography to be 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. Several examples of the use of FISH-MAR in natural and engineered systems are reviewed. The capabilities and limitations of this technique for linking microbial community structure and function are discussed.