Types of Aquatic Organisms - Freshwater Ecology: Concepts and Environmental Applications - page 117

nomic trees generated by morphology (e.g., cyanobacteria), reasonably
good agreement occurs between results from conventional techniques and
RNA analysis (Giovannoni et al., 1988; Taylor, 1999).
When the rRNA sequence is known for a particular species, this in-
formation can be used for in situ identification of species. A complemen-
tary DNA strand is synthesized that matches a unique section of the DNA
that codes for the rRNA, and a label such as a fluorescent or radioactive
molecule is attached to the end of the complementary strand. The labeled
probe then will attach selectively to target organisms in the natural envi-
ronment with the complementary sequence and can be used for rapid
in situ identification.
Use of molecular techniques based on rRNA will likely become more
common and more feasible for aquatic ecologists. Scientists first successfully
determined RNA sequences from environmental samples taken from open-
ocean (Giovannoni et al., 1990) and hotspring organisms (Ward et al.,
1990). Interestingly, many of the rRNA sequences found in natural envi-
ronments are from organisms that have not been grown successfully in the
laboratory. In a particularly impressive application of modern technology, a
known rRNA sequence was used to label a bacterium from the natural en-
vironment. Following labeling, “optical tweezers” (lasers used to manipu-
late microscopic particles) were used to isolate and culture individual marked
cells of known bacterial species (Huber et al., 1995). In the future, scien-
tists will use related techniques for microbes and other groups whose taxo-
nomic identity is difficult to establish in situ. For example, aquatic ecolo-
gists rarely identify the larvae of chironomid midges to species because
identification is very time-consuming and requires considerable experience.
A rapid molecular method for nonsystematists would be very helpful in wa-
ter quality studies using midge larvae as biological indicator species.
motile, and exhibit behavior. This blurred traditional distinctions between an-
imals and plants. Electron microscopy allowed definitive differentiation be-
tween organisms with complex inner architecture (eukaryotes) and those with
more simple cells (prokaryotes). Recently, analysis of rRNA and other bio-
logical molecules has revealed that the Archaea split from the Eukarya shortly
(relative to the 4-billion-year-old Earth) after they diverged from the Bacteria
(Fig. 7.1). Such analyses have also revealed that the Bacteria, Archaea, and
Eukarya should be assigned to super kingdoms or domains, not to the tradi-
tional kingdoms (Woese et al., 1990). If Eukarya is assigned a kingdom-level
designation, then it retains the name Eukaryota. The interpretation of rRNA
data has recently been called into question, however, because of possible
transfer of genetic material among organisms over evolutionary time (Williams
and Embley, 1996; Doolittle, 1999). The issue remains to be resolved, but at
least the idea of three domains allows an appreciation of the tremendous di-
versity of organisms in the Eukarya and Archaea.
The Eukarya apparently formed from the union of ancestral cells of Eu-
karya and Bacteria (Sapp, 1991). This idea is called the serial endosymbiosis
theory and was developed through the work of Dr. Lynn Margulis. Most