1. Microbial Evolution and Systematics
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. 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.
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.

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

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

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. The phylogeny of microorganisms is their evolutionary relationships.
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. SSU (small subunit) RNA sequencing is synonymous with 16S or 18S sequencing.
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.
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 Evolution  Microbial 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
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.

51. The Species Concept in Microbiology
The species concept applies to prokaryotes as well as eukaryotes, and a similar taxonomic hierarchy exists.

52. Groups of genera (singular: genus) are collected into families, families into orders, orders into classes, classes into phyla (singular: phylum), and so on up to the highest-level taxon, the domain.

53. It has been proposed that a prokaryote whose 16S ribosomal RNA sequence differs by more than 3% from that of all other organisms (that is, the sequence is less than 97% identical to any other sequence in the databases), should be considered a new species (Figure 11.25).

54. Relationship between 16S ribosomal RNA sequence similarity and genomic DNA:DNA hybridization

55. Bacterial speciation may occur from a combination of repeated periodic selection for a favorable trait within an ecotype and lateral gene flow (Figure 11.26).

56. A model for bacterial
speciation

57. The model for speciation shown is based solely on the assumption of vertical (mother to daughter) gene flow. However, bacterial speciation is also affected to some degree by lateral (horizontal) gene transfer. Lateral flow is the transfer of genes between species by conjugation, transduction, and transformation.

58. Table 11.5 gives the taxonomic hierarchy for the purple sulfur bacterium Allochromatium warmingii.

60. Table 11.6 lists taxonomic ranks and numbers of known prokaryotic species.

62. Nomenclature and Bergey's Manual
Following the binomial system of nomenclature used throughout biology, prokaryotes are given descriptive genus names and species epithets.

63. Formal recognition of a new prokaryotic species requires deposition of a sample of the organism in a culture collection and official publication of the new species name and description. Bergey's Manual of Systematic Bacteriology is a major taxonomic compilation of Bacteria and Archaea.