CHAPTER 11 Microbial Evolution and Systematics

1. CHAPTER 11 Microbial Evolution and Systematics

2. Early Earth, the Origin off Life, and Microbial Diversification Planet Earth is approximately 4.6 billion years old. The first evidence for microbial life can be found in rocks about 3.86 billion years old. • Stromatolites are fossilized microbial mats consisting of layers of filamentous prokaryotes and trapped sediment.

3. Early Earth was anoxic and much hotter than the present Earth. The first biochemical compounds were made by abiotic syntheses that set the stage for the origin of life. By comparing ancient stromatolites with modern stromatolites, it has been concluded that filamentous phototrophic bacteria, perhaps relatives of the green nonsulfur bacterium Chloroflexus, formed ancient stromatolites.

4. Primitive Life: The RNA World and Molecular Coding The first life forms may have been self-replicating RNAs (RNA life). These were both catalytic and informational. Eventually, DNA became the genetic repository of cells, and the three-part system—DNA, RNA, and protein—became universal among cells (Figure 11.5).

5. Possible mechanileifsm of evolution of life

6. Primitive Life: Energy and Carbon Metabolism Primitive metabolism was anaerobic and likely chemolithotrophic, exploiting the abundant sources of FeS and H2S present (Figure 11.6). Carbon metabolism may have included autotrophy.

7. Energy generating scheme for primitive cell

8. Landmarks of biological evolution Oxygenic photosynthesis led to development of banded iron formations, an oxic environment, and great bursts of biological evolution (Figure 11.8).

9. Eukaryotes and Organelles: Endosymbiosis • Mitochondria and chloroplasts, the principal energy-producing organelles of eukaryotes, arose from the symbiotic association of prokaryotes of the domainBacteria within eukaryotic cells, a process called endosymbiosis (Figure 11.9). The eukaryotic nucleus and mitotic apparatus probably arose as a necessity for ensuring the orderly partitioning of DNA in large-genome organisms.

10. Mitochondria arose from the Proteobacteria, a major group of Bacteria. • Origin of the modern life

11. Assuming that an RNA world existed, self-replicating entities have populated Earth for over 4 billion years (Figure 11.10).

12. Self replicating entities on earth

13. Methods for Determining Evolutionary Relationships, Evolutionary Chronometers, The phylogeny of microorganisms is their evolutionary relationships. • Certain genes and proteins are evolutionary chronometers—measures of evolutionary change. Comparisons of sequences of ribosomal RNA can be used to determine the evolutionary relationships among organisms.

14. Differences in nucleotide or amino acid sequence of functionally similar (homologous) macromolecules are a function of their evolutionary distance. • Phylogenetic trees based on ribosomal RNA have now been prepared for all the major prokaryotic and eukaryotic groups. SSU (small subunit) RNA sequencing is synonymous with 16S or 18S sequencing. • A huge database of rRNA sequences exists. For example, the Ribosomal Database Project (RDP)contains a large collection of such sequences, now numbering over 100,000.

15. Ribosomal RNA Sequences as a Tool of Molecular Evolution Comparative ribosomal RNA sequencing (Figure 11.11) is now a routine procedure involving the amplification of the gene encoding 16S ribosomal RNA, sequencing it, and analyzing the sequence in reference to other sequences (Figure 11.12).

16. Ribosomal RNA

17. rRNA sequencing

18. Two major treeing algorithms are distance and parsimony (Figure 11.13).

23. Signature Sequences, Phylogenetic Probes, and Microbial Community Analyses Signature sequences, short oligonucleotides found within a ribosomal RNA molecule, can be highly diagnostic of a particular organism or group of related organisms. Table 11.1 shows signature sequences from 16S or 18S rRNA defining the three domains of life.

25. Signature sequences can be used to generate specific phylogenetic probes, useful for fluorescent in situ hybridization (FISH) or microbial community analyses.

26. Microbial EvolutionMicrobial Phylogeny Derived from Ribosomal RNA Sequences The universal phylogenetic tree (Figure 11.16) is the road map of life.

27. Universal phylogenetic tree

28. Life on Earth evolved along three major lines, called domains, all derived from a common ancestor. Each domain contains several phyla. Two of the domains, Bacteria and Archaea, remained prokaryotic, whereas the third, Eukarya, evolved into the modern eukaryotic cell.

29. Characteristics of the Domains of Life Although the three domains of living organisms were originally defined by ribosomal RNA sequencing, subsequent studies have shown that they differ in many other ways. • In particular, the Bacteria and Archaea differ extensively in cell wall and lipid chemistry (Figure 11.18) and in features of transcription and protein synthesis (Table 11.2).

30. Lipids in cell wall

32. Table 11.3 summarizes a number of other phenotypic features, physiological and otherwise, that can be used to differentiate organisms at the domain level.

35. Microbial Taxonomy And Its Relationship To Phylogeny Classical Taxonomy Conventional bacterial taxonomy places heavy emphasis on analyses of phenotypic properties of the organism (Table 11.4).

37. To identify an organism, one must assess several of its phenotypic properties, from general to specific (Figure 11.20).

39. Determining the guanine plus cytosine base ratio (GC ratio) of the DNA of the organism can be part of this process (Figure 11.21).

41. Chemotaxonomy Molecular taxonomy involves molecular analyses of specific cell components.

42. These include, among others, DNA:DNA hybridization (Figure 11.22), ribotyping and multilocus sequence typing (MLST) (Figure 11.23), and fatty acid analyses, such as fatty acid methyl ester (FAME) analysis (Figure 11.24).

43. Genomic hybridization as taxonomic tool

46. Ribotyping

47. Multilocus sequence typing

49. Fatty acid methyl ester (FAME) analysis

50. Genomic hybridization measures the degree of sequence similarity in two DNAs and is useful for differentiating very closely related organisms where rRNA sequencing may not be definitive.