On long time-scales, of centuries to millennia, environmental 

 changes affect the structure of biological communities within 

 ecosystems by altering the species composition through natural 

 selection. The functional stability of ecosystems includes species 

 composition, functional redundancy among species, genetic diversity 

 within species, and numerical abundance among the species. Changes 

 in community structure and diversity due to natural and human 

 perturbations may or may not have a measurable effect on ecosystem 

 function. To understand the ecosystem changes, ecologists must be 

 able to measure changes in the diversity, abundance, and degree of 

 functional redundancy of organisms. 



The classical model of ecosystem change following a 

 disturbance is portrayed by successional changes among organisms 

 that are driven by patterns of migration, competition, and 

 environmental modification by alternative organisms. This process 

 results in a dynamic community, usually assumed to be best adapted 

 temporally and spatially. Over the past two decades, virtually 

 every aspect of this model has been seriously questioned. Notions 

 of long-term environmental stability have been shattered by 

 paleoecological studies that reveal constant climatic change at 

 temporal scales ranging from decadal oscillations to 100-millennia 

 ice ages. In many communities, changes do not lead to biotic 

 stability. Indeed, changes in ecosystems may increase the 

 likelihood of disturbance, as occurs, for example, in forests which 

 accumulate flammable fuels. The resulting cycles of disturbance 

 may generate complex arrays of "metastable" community 

 configurations . 



For microbial communities within ecosystems, conceptual models 

 of successional change are based primarily on competition for 

 limited multiple resources. However, documenting succession, which 

 is only the first step in understanding the ecosystem's dynamics 

 and self-adaptation, has been severely hampered by the inability of 

 ecologists to identify, enumerate, and characterize the myriad of 

 microbes present. Only a small fraction (< 1%) of microbes that 

 live in nature can be readily cultivated in the laboratory. 

 Moreover, it has become increasingly clear that many microbial 

 communities evolved with complex interactions, forming so-called 

 consortia. Techniques of molecular biology have been especially 

 promising in enabling microbial ecologists to identify and 

 enumerate microbes, based on the characterization of nucleic acids, 



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