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Chapter 35 : Community Structure: Bacteria and Archaea
This chapter outlines the various approaches that are used to determine community structure and some guidelines regarding which methods may be most appropriate for specific aquatic environments and specific scientific questions. It describes new molecular biological and other highly technical approaches in detail, even though they are still under development, because they are likely to become particularly important in the future. The oldest method for obtaining information on microbial community structure is to examine the sample with a microscope and characterize the microbes by their morphology. The most common traditional method of determining community structure involves culturing the organisms from the habitat in question and identifying the cultures by standard techniques. Immunological approaches have been used primarily to characterize and count nitrifying bacteria and cyanobacteria. The molecular size distribution pattern of low-molecular weight RNA (including tRNAs and 5S rRNA) is thought to be unique within narrow phylogenetic groups of microorganisms. The PCR methods have been used with samples from sediments and microbial mats, as well as deep-sea holothurian guts, often showing unexpected bacterial and archaeal diversity. Some studies have used information about the 16S rRNA clones short of partial or full sequences. There is still a question about possible biases and errors in the molecular methods. There is also the question of quantitative biases. In the quantitative analysis of community structure, oligonucleotide probes are powerful tools that avoid possible biases in cloning and yield a more direct measure of the target groups of interest.