Types of Aquatic Organisms - Freshwater Ecology: Concepts and Environmental Applications - page 116

METHOD 7.1.
Using Ribosomal RNA Analysis for Identification of Organisms
Ribosomal ribonucleic acid (rRNA) sequence comparison has been used in-
creasingly as a taxonomic tool, particularly for microorganisms. Several
RNA molecules occur in each ribosome (the site for protein synthesis in
the cell). The 16S rRNAs in bacteria and 18S rRNAs in eukaryotes are gen-
erally used for taxonomic comparisons. There are several advantages of the
use of rRNA. The molecules are found in all living organisms and have
some sequences that are very conservative, meaning they retain some sec-
tions that all organisms have in common. The rRNA molecules also con-
tain regions that change more rapidly over evolutionary time and can be
used for detailed analysis at the species or subspecies level. Finally, molec-
ular methods have developed in which small amounts of rRNA from nat-
ural populations can be amplified and analyzed.
The technique is based on comparing sequences of rRNA molecules from
different organisms. The greater the time since evolutionary divergence of
species, the more the sequences will vary. The rRNA (Fig. 7.3) has specific
sections that are required for the function of the molecule and others that are
less essential. The sections of the rRNA that are essential to protein synthe-
sis are highly conserved (i.e. their nucleotide sequence varies little among
species) because mutations in these regions are usually fatal. Thus, a taxono-
mist needing to make kingdom-level comparisons would choose a highly con-
served section of the rRNA, and one distinguishing among closely related
species would choose a section that accumulates mutations more rapidly.
Comparison of rRNA sequences is particularly useful for microbes for
which taxonomy is difficult because of the small degree of morphological
variation. In cases in which the technique can be compared to the taxo-
The most recent taxonomic methods use biological molecules, such as
DNA, RNA, lipids, and proteins, to distinguish species. An excellent dis-
cussion of these and other taxonomic techniques can be found in Graham
and Wilcox (2000). One of the most successful methods relies on the RNA
found in ribosomes for taxonomic determinations (Method 7.1). In the fu-
ture, machines may be developed that require only a small tissue sample
or a sample of a few cells for rapid definitive identification of many species.
MAJOR TAXONOMIC GROUPS
Three major groups of organisms have been proposed at the broadest
level of classification: the Eukarya (eukaryotes), the Bacteria, and the Archaea
(Woese et al., 1990). The Bacteria and Archaea were known formerly as the
Prokaryota. Before microscopic and chemical recognition of the unique cel-
lular composition of bacteria, organisms were classified into animals (mobile)
or plants (sedentary and green). After light microscopy became established,
this classification became difficult because many microbes are photosynthetic,