Molecular characterization of microbial communities would be of enormous value if the presence of a particular sequence or organism could be related unambiguously to its function in the soil. In some cases, phylogenetic groupings are informative. For example, all bacilli form resistant spores and the majority of rhizobia fix N2. However, individual taxonomic groups can display considerable physiological versatility, and many functional characteristics are distributed among varied and evolutionarily distant groups. In addition, we know little of the physiological characteristics of novel groups and subgroups.
Even if cultivated representatives of all phylogenetic groups were available, a number of other issues must be considered for prokaryotes. The ordering and naming of hierarchical groups largely follow those for higher organisms, with the species as the basic unit of classification. For higher organisms, the species is defined through the Biological Species Concept and the ability of members within a species to interbreed and inability to breed with members of other species (Cohan, 2002). The lack of sexual reproduction mechanisms in prokaryotes prevents application of this concept, with methodological and conceptual implications for our understanding of the development of distinct phylogenetic groups, evolution, and diversity. Prokaryotes can transfer genes by "lateral (or horizontal) gene transfer" (see Cell Structure), which bypasses standard evolutionary processes (mutation and selection), which can have an enormous influence on microbial community structure and activity. The most obvious example of this is the spread of plasmid-borne antibiotic resistance under selective pressure. Lateral gene transfer is not uncommon, particularly in highly active regions of the soil such as the rhizosphere. Nevertheless, all members of a particular (cultured) taxonomic unit (e.g., species) have many phe-notypic characteristics in common and this can help in relating their presence to their ecosystem function.
In describing the characteristics of prokaryotes, we will necessarily focus on established, cultivated groups, highlighting the ecological relevance of these characteristics and demonstrating importance through species diversity and functional diversity and assessing the extent to which these can be related. Understanding the characteristics of the "significant majority" of other prokaryotes awaits new techniques for their isolation and/or cultivation-independent analysis.
general features of prokaryotes
The majority of prokaryotes are smaller than eukaryotes and cell size per se has significant influence on their ecology, methods of their study, and perceptions of their importance. Prokaryotic cells are in the order of several micrometers in length or diameter, although there are notable exceptions (Schulz and Jorgensen, 2001). The fact that bacteria cannot be seen with the naked eye fools many into believing that they are not important in soil processes and leads to approaches in which prokaryotes are treated as a "black box," with little consideration of their enormous species richness and diversity. Microscopic size also makes observational studies difficult and leads to study of populations or communities, rather than individuals, and to estimating characteristics (e.g., cell concentrations) on the basis of properties of samples.
Small size is associated with high surface area:volume ratio, which explains, in part, the ability of prokaryotes to sequester nutrients at extremely low concentrations. Cells are in intimate contact with their physical and chemical environment. Although homeostatic mechanisms exist for maintaining internal solute concentrations and pH, prokaryotes respond much more rapidly to, and are influenced more by, changes in environmental conditions than the more complex cells of eukaryotes. This, in turn, necessitates greater consideration of microenvironments or microhabitats and the physicochemical characteristics of the environment immediately surrounding the cell. The 1-10pm scale will be of greater significance for growth and activity of unicellular organisms than for bulk soil properties. Again, this has methodological implications. Small size also influences the distribution and movement of organisms. For example, prokaryotes are able to penetrate and colonize small soil pores, potentially protecting them from predation.
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