Methods for sampling and analyzing wetland soil bacterial community

Document Type

Article

Publication Date

1-1-2013

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 nextgeneration 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.

Publication Source (Journal or Book title)

Wetland Techniques Volume 2 Organisms

First Page

59

Last Page

92

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