Screening phylogenetic and functional marker genes in soil microbial ecology.

Many of the ecosystem services are soil associated with microbes playing a predominant role. Nevertheless, our current knowledge of microbial contribution to ecosystem processes is still limited, partly because in the past centuries research was mostly based on culture-dependent methods, being oblivious of the vast un-cultivable microbial majority as proven during the last decades. Current molecular biology advances provide us with the ability to screen for microbial identities or functions by targeting marker genes in nucleic acid extracts of environmental samples, therefore partly bypassing previous methodological limitations. Topics addressed here aim at providing an overview of methodologies and concepts related to marker gene screening from environmental samples. Such are the description of marker gene categories, examples of their use in soil environments and the description of marker gene screening state-of-the-art methodologies and specifications. Finally we will exemplify the use of late methodologies for the case of the bacterial small ribosomal subunit screening in soil environments.