ABSTRACT
Microbial communities are responsible for processes that are essential for the functioning of ecosystems. The activity of a microbial community as a whole is regulated by environmental factors and depends on the activities of their individual members and populations and interactions amongst them. Microbial communities are thus complex, metabolically flexible and highly adaptable to changing environmental conditions, with their function finely regulated at the molecular level. The complexity of communities makes the analysis of microbial processes in the environment an important challenge for microbial ecologists. In addition to classical ecophysiological approaches that rely on the detection of products resulting from a particular process and the measurement of transformation rates (1), we now possess sophisticated and powerful molecular biology techniques to analyze microbial function in the environment (2, 3), such as the analysis of gene expression via detection of mRNA after reverse transcription-polymerase chain reaction (RT-PCR). Since prokaryotic gene expression is a finely regulated process (4, 5), detection of transcripts for a given gene constitutes significant evidence of the occurrence of a given biological process within the environment. Recent years have seen a significant increase in the number of studies reporting the analysis of microbial gene expression by RT-PCR in environmental systems. The majority of these studies can be subdivided into three main groups with respect to the type of genetic systems being analyzed: (i) analysis of gene expression in pathogenic bacteria, e.g. the human pathogens Staphy-
lococcus aureus and Helicobacter pylori (6, 7); (ii) detection and analysis of expression of genes involved in relevant biogeochemical
processes such as methanotrophy, nitrogen fixation, nitrification, denitrification and carbon fixation (8-11);
(iii) investigation of the expression of genes involved in the biodegradation of environmental pollutants, such as aromatic hydrocarbons (12-14).
