Molecular biology: A linkage between microbial ecology, general ecology and organismal biology

The field of microbial ecology has been developing rapidly, largely owing to the introduction of new molecular methods for identifying individuals, species and populations of microorganisms in nature. In contrast to traditional methods, the new ones do not require the isolation and culture of organisms from the environment. With many of the new methods, genotypes and species of microorganisms can be identified by using 'marker' sequences of nucleic acids that can be related to those of other organisms by applying phylogenetic methods. Thus molecular techniques provide information on both the structure and evolutionary relationships of organisms in microbial communities. Methods are also available for analyzing gene expression and metabolic activities of microbial communities in situ. They make it possible to link microbial diversity to ecological processes and to bridge the gap between microbiology in the laboratory, microbial ecology and general ecology. The development of microbial ecology has been highly dependent on information obtained from studies of microorganisms in pure or mixed cultures. These studies have been focused on identifying genes, enzymes, metabolites, etc., involved in important microbial interactions and ecological processes, such as parasitism, symbiosis, decomposition and nitrogen transformation. Recently this 'organism-oriented' branch of microbial ecology has been strongly stimulated by the results obtained within the large genome projects. Large-scale sequencing and functional analyses of genes, transcripts, proteins and metabolic pathways are being carried out on a number of microorganisms, including the well-characterized 'model organisms' (such as Saccharomyces cerevisiae) as well as several species of substantial ecological importance. A major future challenge of 'post-genome' projects will be to decipher the relationships between genotypes and phenotypes, and to link molecular mechanisms to adaptive variation. These are also central problems in ecology. The strong connection between microbial ecology and molecular biology should inspire us to make further advances in these areas of ecology as well as to integrate general ecology more closely with organismal biology.