Some Problems Posed by Natural Environments for Monitoring Microorganisms

The history and emergence of microbiology as a scientific discipline are intimately linked with developments of methods for isolation, enrichment, growth, and maintenance of microorganisms in the laboratory as pure cultures to enable subsequent biochemical and genetic analyses. This approach has been extremely successful for the manipulation and exploitation of microorganisms in terms of disease control and eradication, development of biotechnological processes, and the evolution of sophisticated molecular genetic techniques. It has also resulted in some bacterial species being studied more than others, and some have become model species, the properties of which are then inferred for all microorganisms. Examples include the widespread use of Escherichia coli (model Gram-negative), Bacillus subtilis (Gram-positive), Streptomyces coelicolor (industrially important mycelial prokaryotes), Saccharomyces cerevisiae (model for yeast), and Aspergillus spp. (widely studied fungus). Unfortunately, it is often the case that experimental protocols developed for model species are not transposable to other bacteria. This gulf is often most apparent when deductions made from organisms grown as pure cultures in the laboratory are assumed to apply to those occurring in natural environments.