Chapter 28 : Phylogeny and Functionality: Taxonomy as a Roadmap to Genes

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Taxonomy, the principles and practice of classification of the organisms that make up biological diversity, enables their detection and identification. The extent to which a general, phylogenetically based taxonomy can be predictive depends on the relative contributions of horizontal and vertical transmission of genes. To exploit this predictive power will depend on one's understanding of biological diversity, the distribution of genes within that diversity, and the ecology and biogeography of the organisms. Taxonomy is a key prerequisite to this understanding. The relationship between taxonomy and genes has been indirect, and views on the distribution of genes across microbial diversity based on observations of phenotypic properties and concepts of inheritance began to be challenged only with the recognition of widespread transfer of antibiotic resistance genes. Biomarkers indirectly reflect the distribution of the genes responsible for their biosynthesis, although additional complexity is often revealed when the specific genes responsible for metabolic processes and products are identified. In the context of bioprospecting, taxonomy has three roles: enabling the classification and then the detection and identification of organisms; predicting metabolic potential; and dereplicating isolates for screening. Much of the recent evidence that lateral gene transfer is extensive has come from statistical comparisons of DNA base sequence data. New high-throughput techniques for phenotypic characterization, whole-genome and multilocus sequencing, microarrays, and subtractive hybridization will define the unit of diversity for prokaryotes—the genome species concept—and provide a roadmap to help guide the new search and discovery strategies.

Citation: Ward A, Goodfellow M. 2004. Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, p 288-313. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch28

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High-Performance Liquid Chromatography
Elongation Factor Tu
16s rRNA Sequencing
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Figure 1

DNA-.DNA homology versus 16S rRNA similarity. Data for actinomycetes, from the literature. Adapted from J. Chun, Ph:D. thesis, University of Newcastle upon Tyne, updated by J . Ε. M. Stach and L. A. Maldonado.

Citation: Ward A, Goodfellow M. 2004. Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, p 288-313. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch28
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Figure 2

Distribution of PUFAs among some members of the family . Adapted from .

Citation: Ward A, Goodfellow M. 2004. Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, p 288-313. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch28
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Figure 3

clade in the streptomycete phylogenetic tree.

Citation: Ward A, Goodfellow M. 2004. Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, p 288-313. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch28
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Figure 4

HPLC profile of secondary metabolites from a representative strain of the clade. ELSD, evaporative light-scattering detector.

Citation: Ward A, Goodfellow M. 2004. Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, p 288-313. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch28
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Figure 5

DNA:DNA homology of members of the clade.

Citation: Ward A, Goodfellow M. 2004. Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, p 288-313. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch28
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Figure 6

Comparative genomics of some members of the clade. Genes present and absent detected by microarrays.

Citation: Ward A, Goodfellow M. 2004. Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, p 288-313. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch28
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