Cultivation-Independent Detection of Genes Present in Soil Bacteria

Authored by: Guo-Chun Ding , Holger Heuer , Kornelia Smalla

Handbook of Soil Sciences Properties and Processes

Print publication date:  November  2011
Online publication date:  November  2011

Print ISBN: 9781439803059
eBook ISBN: 9781439803066
Adobe ISBN:

10.1201/b11267-48

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Abstract

The development of methods to extract DNA directly from soil samples opened new dimensions of studies on microbial communities in soil. The molecular analysis of soil DNA can provide information on the microbial community composition or on the presence and on the relative abundance of functional genes, for example, of genes involved in N-cycling, antibiotic resistance genes, degrading genes, or plasmid replicon-related sequences. DNA-based analysis of soils led to the discovery of many taxa that are abundant in soils but had not been studied before as they do not easily form colonies on plates. This chapter is exclusively devoted to the detection of genes in DNA directly extracted from soil. Crucial prerequisites of the cultivation-independent detection of genes in soil are appropriate sampling strategies and DNA extraction protocols. Therefore, the subsequent two paragraphs will briefly address these topics before discussing the potentials and limitations of methods for targeted or untargeted detection of genes.

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