The Global Inventory of Microbial Diversity and the Great Plate Count Anomaly

Cellular microorganisms can be categorized based on their cell morphology and ultrastructure into two groups, namely the prokaryotes (Bacteria and Archaea) and the microbial eukaryotes (Eukarya). However, it is important to emphasize that 'prokaryotes' do not represent a coherent evolutionary grouping. The term prokaryote is, however, a useful and pragmatic shorthand that is widely used to describe members of the Bacteria and Archaea which are as evolutionarily distinct from each other as they are from eukaryotic organisms. Microorganisms in general have short generation times, which, coupled with huge population sizes, offer enormous potential to accumulate genetic mutations over relatively short time periods. In addition, despite the absence of sex in prokaryotes and in many of the microbial eukaryote lineages, it is apparent that their evolution is dramatically influenced by lateral gene transfer.

Given this potential to accumulate genetic mutation and the fact that microorganisms were the only life-forms for the majority of the Earth's history, that is, from around 3.5-0.5 billion years ago, one might expect that microbial diversity should be considerably greater than the diversity of higher life-forms. This is, however, a matter of considerable and often polarized debate which is engendered to some degree by the still poor sampling of global microbial diversity. Nevertheless, it is clear from comparative analysis of sequences of homologous genes, in terms of the deeper branching lineages if not the total number of species, that the tree of life is dominated by microorganisms and that, in this sense, microbial diversity far outstrips the diversity of Metazoa and plants (Figure 1). Comparative analysis of homologous genes for the inference of evolutionary relationships was first developed by Linus Pauling; however, the zenith of this approach was reached when Carl Woese and others recognized that small subunit ribosomal RNA (rRNA; 16S rRNA in bacteria and archaea and 18S rRNA in eukaryotes) was present in all cellular organisms and their comparative analyses could provide a universal framework for examining evolutionary relationships between all life-forms.

The comparative analysis of small subunit rRNA over the last two decades has expanded our understanding of a

Figure 1 A 'tree of life' derived from a comparative analysis of small subunit rDNA gene sequences constructed using the ARB software package and database (http://arb-home.de). The tree shows the deeper branching lineages within the bacterial, archaean, and eukaryotic domains. Note that with the exception of the plant and animal lineages all other lineages are comprised of microbial species.

Figure 1 A 'tree of life' derived from a comparative analysis of small subunit rDNA gene sequences constructed using the ARB software package and database (http://arb-home.de). The tree shows the deeper branching lineages within the bacterial, archaean, and eukaryotic domains. Note that with the exception of the plant and animal lineages all other lineages are comprised of microbial species.

Figure 2 A phylogenetic tree showing the deeper branching lineages within the bacterial domain. The tree was constructed using the ARB software package (http://arb-home.de) and is based on a comparative analysis of 16S rDNA gene sequences. Valid phyla either described in the taxanomic outline of Bergey's manual by Garrity et al. in 2004 or described by Hugenholtz in 2002 are shown in italics. These phyla have cultured representatives. Where possible, candidate phyla with no-cultured representatives have been assigned names (block capitals) Note that the number of lineages shown in this tree is a significant increase on the 18 identified by Carl Woese in 1987.

Figure 2 A phylogenetic tree showing the deeper branching lineages within the bacterial domain. The tree was constructed using the ARB software package (http://arb-home.de) and is based on a comparative analysis of 16S rDNA gene sequences. Valid phyla either described in the taxanomic outline of Bergey's manual by Garrity et al. in 2004 or described by Hugenholtz in 2002 are shown in italics. These phyla have cultured representatives. Where possible, candidate phyla with no-cultured representatives have been assigned names (block capitals) Note that the number of lineages shown in this tree is a significant increase on the 18 identified by Carl Woese in 1987.

number of microbial phyla (Figure 2). Most of these newly discovered phyla are represented by organisms that have, so far, not been cultivated in the laboratory (they have only been identified on the basis of rRNA sequences recovered directly from environmental samples) and consequently the vast majority of prokaryotic diversity remains to be fully characterized. Eukaryotic microbial species are generally considered to be more tractable to traditional identification techniques. They are generally larger and cell morphology and ultrastructure can be used to identify and enumerate individual species. Nevertheless it is known that a single morphos-pecies can encompass considerable genetic diversity. Moreover, the application of culture-independent methods for determining the diversity of microbial eukaryotes is also uncovering previously unidentified and uncultured major lineages. The new lineages have tended to be picoeukaryotes and suggest it is possible that we have only scratched the surface of microbial eukatyote diversity.

Up until the end of the twentieth century, the study of microbial ecology was dominated by cultivation-based approaches that can trace their ancestry to the pure culture philosophy of Robert Koch that had proved so successful in identifying and understanding the causative agents of many important diseases. However, it is now clear that this approach is left wanting when brought to bear upon the cultivation of the dominant microorganisms inhabiting a wide range of environments. This is most clearly illustrated by data comparing the abundance of bacteria measured by direct observation in samples from natural environments compared with abundances determined on the basis of growth in artificial laboratory growth media. The direct counts are typically 1-2 orders of magnitude greater than figures obtained from growth-dependent measurements. This has been elegantly dubbed 'the great plate count anomaly'. Furthermore, the organisms that do grow in conventional laboratory growth media are rarely those that are dominant in the environment and have been described by Carl Woes as a zoo of monsters, laboratory freaks that best performed the (physiological) feats required of them. The difficulty in detecting identifying and quantifying most microorganisms as they occur in nature distinguishes microbial ecology from many areas of classical ecology, and matching dominant organisms present in an environment to the environmental conditions and resources which dictate their distribution and abundance is often a considerable challenge. Even when an organism can be cultivated in the laboratory, its properties determined may not necessarily reflect the activities and physiology of its counterparts in the environment, where resource competition, environmental heterogeneity, predation, and other interactions occur.

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