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Gideon M. Wolfaardt, Department of Microbiology, University of Stellenbosch, Private Bag X1, 7602 Stellenbosch, South Africa,
Darren R. Korber, Department of Applied Microbiology & Food Science, University of Saskatchewan,Saskatoon, SK, Canada S7N 5A8,
Subramanian Karthikeyan, Department of Applied Microbiology & Food Science, University of Saskatchewan,Saskatoon, SK, Canada S7N 5A8,
Douglas E. Caldwell, Department of Applied Microbiology & Food Science, University of Saskatchewan,Saskatoon, SK, Canada S7N 5A8
It has been shown that microbial communities contribute extensively to the attenuation, mineralization and transport of both organic and inorganic contaminants in the environment. The development of biofilms by microbial communities is often a key factor contributing to the overall efficiency of these processes (Rothemund et al., 1996). For instance, bacterial biofilms are able to accumulate metals through various mechanisms (Marques et al., 1991; Sillitoe et al., 1994). Liehr et al. (1994) showed that biofilms formed by algae could concentrate metals at levels more than four orders of magnitude higher than those in the surrounding water.
The potential of bioremediation as an alternative to physical and chemical remediation strategies has resulted in a significant amount of research effort on degradative biofilms. Although much emphasis has been placed on the degradation of xenobiotic compounds, the knowledge gained through these studies has also contributed to an improved understanding of processes involved in the degradation of naturally occurring molecules as well as nutrient cycling in general. Tank & Webster (1998) suggested that competition for nutrients might regulate heterotrophic microbial processes in natural streams. In their study, they found that nutrient immobilization by leaves partially inhibited other heterotrophic processes, as evidenced by low microbial respiration, fungal biomass and extracellular enzyme activity among wood biofilms in the presence of leaf litter. Lawrence et al. (1998) stressed the applicability of knowledge gained through the study of naturally occurring attenuation mechanisms to remediating contaminated environments. Clearly, the study of degradative biofilms is of both fundamental and applied interest.
The need for laboratory studies of biofilm communities
If microbial ecology is to move forward, it must go beyond the reduction of the complexities of bacteria into merely isolated cell lines, enzymes, and genetic sequences. A century of pure culture studies has provided extremely detailed information on the biochemistry, physiology and genetics of bacteria. What remains to be determined is how they function as successful members of interacting communities in biofilms and how microbial communities function as components of the environment.
Filling this gap in knowledge involves more than the in situ enumeration of cells, molecules, and genetic sequences. It requires that microbial communities be considered as functional units of ecological activity. Individual microorganisms are often tightly coupled with other community members through a complex network of interactions. The genetic programming of each species may be considered to be a reproductive strategy formulated over 2.5 billion years of natural selection, and intricately intertwined with the survival of other organisms (Margulis 1981). Consequently, the most rigorous measure of understanding must involve not only the cultivation of isolated cell lines, but also the successful cultivation and characterization of dynamic microbial communities, complete with their predators and parasites.
End of the pure culture era
The primary axiom of bacteriology is that organisms must be isolated prior to their identification and study, and prior to the description of new species (Koch 1881, 1884). This axiom is so pervasive that it impacts protozoology, mycology and algology as well as bacteriology.
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