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Methods for Sampling and Analyzing Wetland Soil Bacterial Community

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Wetland Techniques

Abstract

Wetland soil, a heterogeneous environment highly modified by its hydrologic condition and vegetation, provides habitats for a variety of aerobic and anaerobic bacteria. Sampling the wetland soil bacterial community involves collection of bulk or rhizosphere soil or both, depending on the purpose of the study. In any case, it is crucial to assure that random, but representative samples are collected to provide meaningful data and to meet the purposes of the study. Approaches to the analyses of the bacterial communities in wetland soils may be divided into two general categories: cultivation-based and cultivation-independent techniques. The first category relies on laboratory cultivation and the second is based on the analyses of indicator molecules such as DNA extracted directly from soil samples. The primary cultivation-independent methods include 16S rRNA gene-based cloning library, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP), and fluorescence in situ hybridization (FISH). More recently, high-throughput technologies, such as next-generation DNA sequencing (e.g., 454 pyrosequencing and Illumina sequencing) and GeoChip, were developed to generate large amounts of genetic information allowing more in-depth and comprehensive assessment of bacterial communities. This chapter focuses on some practical approaches commonly used for sampling and analyzing bacterial communities in wetland soils.

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Authors and Affiliations

  1. Department of Environmental Sciences, School of the Coast and Environment, Louisiana State University, 1255 Energy, Coast and Environment Building, Baton Rouge, LA, 70803, USA

    Aixin Hou

  2. Environmental Sciences Institute, Florida A&M University, 1515 Martin Luther King Boulevard, Tallahassee, FL, 32307, USA

    Henry N. Williams

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  1. Forestry & Natural Resources & Environmental Research Center, West Virginia University, Morgantown, West Virginia, USA

    James T. Anderson

  2. Department of Natural Resource Ecology a, Oklahoma State University, Stillwater, Oklahoma, USA

    Craig A. Davis

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Hou, A., Williams, H.N. (2013). Methods for Sampling and Analyzing Wetland Soil Bacterial Community. In: Anderson, J., Davis, C. (eds) Wetland Techniques. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6931-1_2

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