Molecular microbial ecology: land of the one-eyed king

Studies of microbial biodiversity have made astounding discoveries of late due to the use of methodologies based on phylogenetic analyses of small subunit ribosomal RNA sequences. Although there are limitations to these methods, they can nonetheless be very useful if these limitations are kept in mind. These limitations range from technical problems such as obtaining representative genomic DNA and suitable primers, to conceptual problems such as defining and using meaningful taxonomic units of diversity (species). Here we discuss several of the limitations inherent in studies of microbial diversity that must be considered when interpreting the results obtained using these approaches.