Use of Molecular Probing to Assess Microbial Activities in Natural Ecosystems

Abstract

Our current understanding of both the natural and man-made microbial world is rudimentary. This is caused to a large extent by our inability to cultivate more than a tiny fraction of the bacteria which can be seen to live in soils, oceans and freshwater ecosystems alike. In most cases it is by no means obvious why this should be so, but it is likely that the exact reasons will be different for the various habitats. Apart from the simple fact that a significant fraction of the cells observed in the field are truly dead, more likely reasons are that microorganisms are so eminently adapted to and dependent on the physicochemical, nutritional and biological conditions in their specific environments that we are bound to fail in attempting to mimic such conditions in the laboratory. Until quite recently this situation implicated that our perception of most natural microbial communities was based entirely on those microbial species which were sufficiently flexible to adapt to the artificial conditions created in the laboratory. (Un)fortunately, we now begin to see how wrong this perception has been, as it relied on species which mostly were not representative of the dominant populations in nature. This insight was achieved by the enormous progress in molecular genetics and the subsequent advent of an almost new discipline within microbiology: molecular microbial ecology. The power of this novel field of microbiological research is that substantial information about the structure, the dynamics and the physiological potential can now be inferred from genetic analysis of the microbes in samples from natural habitats without the need to cultivate them (Sayler and Layton, 1990; Amann et al., 1995; Pace, 1996).