Microbes and Metabolism - Environmental Biotechnology: Theory and Application - page 13

to be dissolved in water, chelation renders the substance unavailable. In some
instances this is a desirable end result and may be viewed as a form of reme-
diation, since it stabilises the contaminant. In other cases it is a nuisance, as
digestion would be the preferable option. Such 'unwanted' immobilisation can
be a major problem in remediation, and is a common state of affairs with aged
contamination. Much research effort is being applied to find methods to reverse
the process.
Degradation is achieved by metabolic pathways operating within an organism
or combination of organisms, sometimes described as consortia. These processes
are the crux of environmental biotechnology and thus form the major part of this
chapter. Enzyme activity operates either through metabolic pathways functioning
within the cell, or excreted by the cell or, isolated and applied in a purified form.
Biological monitoring utilises proteins, of which enzymes are a subset, pro-
duced by cells, usually to identify, or quantify contaminants. This has been
developed into an expanding field of biosensor production.
Who are the biological players in these processes, what are their attributes
which are so essential to this science and which types of biological material are
being addressed here? The answers to these questions lie throughout this topic
and are summarised in this chapter.
The players
Traditionally, life was placed into two categories - those having a true nucleus
(eukaryotes) and those that do not (prokaryotes). This view was dramatically
disturbed in 1977 when Carl Woese proposed a third domain, the archaebacteria,
now described as archaea, arguing that although apparently prokaryote at first
glance they contain sufficient similarities with eukaryotes, in addition to unique
features of their own, to merit their own classification (Woese and Fox, 1977;
Woese, Kandler and Wheelis 1990). The arguments raised by this proposal con-
tinue (Cavalier-Smith, 2002) but throughout this topic the classification adopted
is that of Woese, namely, that there are three divisions: bacteria, archaea (which
together comprise prokaryotes) and eukaryotes. By this definition, then, what are
referred to throughout this work simply as 'bacteria' are synonymous with the
term eubacteria (meaning 'true' bacteria).
It is primarily to the archaea, which typically inhabit extreme niches with
respect to temperature, pressure, salt concentration or osmotic pressure, that a
great debt of gratitude is owed for providing this planet with the metabolic
capability to carry out processes under some very odd conditions indeed. The
importance to environmental biotechnology of life in extreme environments is
addressed in Chapter 3.
An appreciation of the existence of these classifications is important, as they
differ from each other in the detail of their cell organisation and cellular processes
making it unlikely that their genes are directly interchangeable. The relevance of
this becomes obvious when genetic engineering is discussed later in this topic
in Chapter 9. However, it is interesting to examine the potentially prokaryotic