The rhizosphere (soil zone influenced by roots) is a complex environment that harbors diverse bacterial populations, which have an important role in biogeochemical cycling of organic matter and mineral nutrients. Nevertheless, our knowledge of the ecology and role of these bacteria in the rhizosphere is very limited, particularly regarding how indigenous bacteria are able to communicate, colonize root environments, and compete along the rhizosphere microsites. In recent decades, the development and improvement of molecular techniques have provided more accurate knowledge of bacteria in their natural environment, refining microbial ecology and generating new questions about the roles and functions of bacteria in the rhizosphere. Recently, advances insoil post-genomic techniques (metagenomics, metaproteomics and metatranscriptomics) are being applied to improve our understanding of the microbial communities at a higher resolution. Moreover, advantages and limitations of classical and post-genomic techniques must be considered when studying bacteria in the rhizosphere. This review provides an overview of the current knowledgeon the study of bacterial community in the rhizosphere by using modern molecular techniques, describing the bias of classical molecular techniques, next generation sequencing platforms and post-genomics techniques. © 2015, Sociedad Chilena de la Ciencia del Suelo. All rights reserved.
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