The energy required to carry out all cellular processes is obtained from ingested food in the case of chemotrophic cells, additionally from light in the case of phototrophs and from inorganic chemicals in lithotrophic organisms. Since all biological macromolecules contain the element carbon, a dietary source of carbon is a requirement. Ingested food is therefore, at the very least, a source of energy and carbon, the chemical form of which is rearranged by passage through various routes called metabolic pathways. One purpose of this reshuffling is to produce, after addition or removal of other elements such as hydrogen, oxygen, nitrogen, phosphorous and sulphur, all the chemicals necessary for growth. The other is to produce chemical energy in the form of adenosine triphosphate (ATP), also one of the ‘building blocks’ of nucleic acids. Where an organism is unable to synthesise all its dietary requirements, it must ingest them, as they are, by definition, essential nutrients. The profile of these can be diagnostic for that organism and may be used in its identification in the laboratory. An understanding of nutritional requirements of any given microbe, can prove essential for successful remediation by bioenhancement.
At the core of metabolism are the central metabolic pathways of glycolysis and the tricarboxylic acid (TCA) cycle on which a vast array of metabolic pathways eventually converge or from which they diverge. Glycolysis is the conversion of the six-carbon phosphorylated sugar, glucose 6-phosphate, to the three-carbon organic acid, pyruvic acid, and can be viewed as pivotal in central metabolism since from this point, pyruvate may enter various pathways determined by the energy and synthetic needs of the cell at that time. A related pathway, sharing some but not all of the reactions of glycolysis, and which operates in the opposite direction is called gluconeogenesis. Pyruvate can continue into the TCA cycle whose main function is to produce and receive metabolic intermediates and to produce energy, or into one of the many fermentation routes.
The principles of glycolysis are universal to all organisms known to date, although the detail differs between species. An outline of glycolysis, the TCA, and its close relative the glyoxalate, cycles is given in Figure 2.1, together with an indication of the key points at which the products of macromolecule catabolism,
or breakdown, enter these central metabolic pathways. The focus is on degrada-tion rather than metabolism in general, since this is the crux of bioremediation. A description of the biological macromolecules which are lipids, carbohydrates, nucleic acids and proteins are given in the appropriate figures (Figures 2.2 – 2.5).
Not all possible metabolic routes are present in the genome of any one organ-ism. Those present are the result of evolution, principally of the enzymes which catalyse the various steps, and the elements which control their expression. However, an organism may have the DNA sequences, and so have the genetic capability for a metabolic route even though it is not ‘switched on’. This is the basis for the description of ‘latent pathways’ which suggests the availability of a
route able to be activated when the need arises, such as challenge from a novel chemical in the environment. Additionally, there is enormous potential for uptake and exchange of genetic information as discussed earlier. It is the enormous range of metabolic capability which is harnessed in environmental biotechnology.
The basis of this discipline is about ensuring that suitable organisms are present which have the capability to perform the task required of them. This demands the provision of optimal conditions for growth, thus maximising degradation or removal of the contaminant. Linked to many of the catalytic steps in the metabolic pathway are reactions which release sufficient energy to allow the synthesis of ATP. This is the energy ‘currency’ of a cell which permits the transfer of energy produced during degradation of a food to a process which may be occurring in a distant location and which requires energy.