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Appl. Environ. Microbiol. doi:10.1128/AEM.01787-07
Copyright (c) 2008, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile

Department of Geological and Environmental Sciences, Stanford University, CA 94305-2115; Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831

^* To whom correspondence should be addressed. Email: hansel{at}seas.harvard.edu.

	Abstract

Spatial heterogeneity in physical, chemical, and biological properties of soils allows for the proliferation of diverse microbial communities. Factors influencing the structuring of microbial communities, including availability of nutrients and water, pH, and soil texture, can vary considerably with soil depth and within soil aggregates. Here we investigate changes in the microbial and functional communities within soil aggregates obtained along a soil profile spanning the surface, vadose zone, and saturated soil environments. The composition and diversity of microbial communities and specific functional groups involved in key pathways in the geochemical cycling of nitrogen, Fe, and sulfur were characterized using a coupled approach involving cultivation-independent analysis of both 16S rRNA (bacterial and archaeal) and functional genes (amoA, dsrAB), as well as cultivation-based analysis of Fe(III)-reducing organisms. Here we find that the microbial communities and putative ammonia-oxidizing and Fe(III)-reducing communities vary greatly along the soil profile, likely reflecting differences in carbon availability, water content, and pH. In particular, the Crenarchaeota are unique to each horizon, sharing a similar distribution and diversity to the putative ammonia-oxidizing archaeal community. Anaerobic microenvironments within soil aggregates also appear to allow for both anaerobic and aerobic-based metabolisms, further highlighting the complexity and spatial heterogeneity impacting microbial community structure and metabolic potential within soils.

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