Appendix III 

 Molecular Approaches to Understanding 

 Community Structure and Function 



Phylogenetic-based Probes to Determine Community Composition and 

 the Abundance and Distribution of Organisms 



Baseline data on community structure and variability are 

 prerequisite for understanding the effects of environmental 

 perturbation on species diversity and community structure and 

 function. Detailed analyses of community structure, diversity, and 

 variability have been largely limited to ecosystems which are 

 spatially and temporally readily described and relatively stable. 

 Terrestrial forest ecosystems, for example, with discrete 

 boundaries and readily identified species, have been extensively 

 characterized by systems ecologists. Our ability to assess the 

 diversity and structure of ecosystems with less easily identified 

 species, extremely small spatial scales, or ill-defined boundaries 

 has been hampered by lack of appropriate methods. To assess the 

 impact of environmental perturbation on ecosystem structure, it is 

 critical to have baseline information on species abundance and 

 variability for which facile identification and quantitation of 

 individual species is necessary. For bacteria, protozoa, and the 

 adult and developmental stages of many metazoans, even reliable 

 species identification may prove difficult. Molecular techniques 

 can resolve some of these difficulties. 



Acquisition of detailed information about community structure, 

 function, and diversity has been hampered by a lack of appropriate 

 methods. In particular, the identification of microorganisms in 

 natural samples generally requires axenic cultivation of the 

 resident organisms, yet we can culture less than 1% of the 

 microorganisms in most environments. Additionally, varying 

 efficiencies in culturing different organisms introduce 

 uncertainties in the enumeration of microorganisms in environmental 

 samples. To address these difficulties, molecular methods are 

 being developed, using gene sequences, in particular of ribosomal 

 RNA (rRNA) , to identify and quantitate microorganisms in natural 

 samples without the need for cultivation. 



If the rRNA sequence of an uncultivated organism can be 

 determined, the evolutionary relatedness of the organism to known 



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