ABSTRACT
Acknowledgments........................................................................................ 332
References.................................................................................................... 332
Previous chapters have addressed the marker used for the assessment of
bacterial diversity, the ribosomal RNA (rRNA), or more precisely the rRNA
of the small subunit (SSU) of the ribosome, in pure cultures and environmental
habitats. This marker molecule proved to be useful as a “molecular clock” or
“document of evolutionary history” [1]. The marker can provide phylogenetic
information about the bacterial species in soils, because ribosomal RNA is an
essential component of the protein-synthesizing machinery in all organisms
(see also Chapter 2). Thus, ribosomal RNA fulfills two major requirements
for a phylogenetic marker molecule: an ubiquitous distribution and a
functional constancy. The 16S rRNA from the small ribosomal subunit, as
well as the 23S rRNA from the large ribosomal subunit, harbor conserved
regions that can be used as primary binding sites to amplify almost the whole
diversity of these molecules by polymerase chain reaction (PCR), even from
complex samples (See Figure 2.2) [2]. The conserved, as well as variable or
hypervariable regions of the rRNA molecule, can also be successfully used as
target sites for oligonucleotide probes specific at the phylum, genus or species
levels [3]. This chapter will examine how methods for detection
of microorganisms can be built on the use of this elegant marker molecule,
placing an emphasis on the methods that allow in situ assessments. However,
before getting to these methods we will examine, how the 16S rRNA genes
can be used in the so-called “full-cycle” approach.
