Microbial Evolution and Systematics

1. Chapter 14 Microbial Evolution and Systematics

2. I. Early Earth and the Origin and Diversification of Life • 14.1 Formation and Early History of Earth • 14.2 Origin of Cellular Life • 14.3 Microbial Diversification: Consequences for Earth’s Biosphere • 14.4 Endosymbiotic Origin of Eukaryotes

3. 14.1 Formation and Early History of Earth • The Earth is ~ 4.5 billion years old • First evidence for microbial life can be found in rocks ~ 3.86 billion years old (southwestern Green land)

4. Ancient Microbial Life 3.45 billion-year-old rocks, South Africa Figure 14.1

5. 14.1 Formation and Early History of Earth • Stromatolites • Fossilized microbial mats consisting of layers of filamentous prokaryotes and trapped sediment • Found in rocks 3.5 billion years old or younger • Comparisons of ancient and modern stromatolites provide evidence that • Anoxygenic phototrophic filamentous bacteria formed ancient stromatolites (relatives of the green nonsulfur bacterium Chloroflexus) • Oxygenic phototrophic cyanobacteria dominate modern stromatolites

6. Ancient and Modern Stromatolites 3.5 billion yrs old Oldest(Western Australia) 1.6 billion yrs old (NorthernAustralia) Modern stromatolites (Western Australia) Modern stromatolites (WesternAustralia) Modern stromatolites (Yellow Stone NP) Figure 14.2

7. More Recent Fossil Bacteria and Eukaryotes From 1 billion yrs old rocks in Central Australia Figure 14.3 Eukaryotic cells Prokaryotes (bacteria)

8. 14.2 Origin of Cellular Life • Early Earth was anoxic and much hotter than present day (over 100 oC) • First biochemical compounds were made by abiotic systems that set the stage for the origin of life

9. Surface origin hypothesis • Contends that the first membrane-enclosed, self-replicating cells arose out of primordial soup rich in organic and inorganic compounds in ponds on Earth’s surface • Dramatic temperature fluctuations and mixing from meteor impacts, dust clouds, and storms argue against this hypothesis

10. Subsurface origin hypothesis • States that life originated at hydrothermal springs on ocean floor • Conditions would have been more stable • Steady and abundant supply of energy (e.g., H2 and H2S) may have been available at these sites

11. Submarine Mound Formed at Ocean Hydrothermal Spring Cooler, more oxidized, more acidic ocean water Hot, reduced, alkaline hydrothermal fluid Figure 14.4

12. Prebiotic chemistry of early Earth set stage for self-replicating systems • First self-replicating systems may have been RNA-based (RNA world theory) • RNA can bind small molecules (e.g., ATP, other nucleotides) • RNA has catalytic activity; may have catalyzed its own synthesis

13. A Model for the Origin of Cellular Life Last Universal Common Ancestor Figure 14.5

14. DNA, a more stable molecule, eventually became the genetic repository • Three-part systems (DNA, RNA, and protein) evolved and became universal among cells

15. Other important steps in emergence of cellular life • Build up of lipids • Synthesis of phospholipid membrane vesicles that enclosed the cell’s biochemical and replication machinery • May have been similar to vesicles synthesized on the surfaces of montmorillonite clay

16. Lipid Vesicles Made in the Laboratory from Myristic Acid vesicle RNAs Vesicle synthesis is catalyzed by the surfaces of montmorillonite clay particles. Figure 14.6

17. Last universal common ancestor (LUCA) • Population of early cells from which cellular life may have diverged into ancestors of modern day Bacteria and Archaea

18. As early Earth was anoxic, energy-generating metabolism of primitive cells was exclusively • Anaerobic and likely chemolithotrophic (autotrophic) • Obtained carbon from CO2 • Obtained energy from H2; likely generated by H2S reacting with FeS or UV light

19. Major Landmarks in Biological Evolution Figure 14.7

20. A Possible Energy-Generating Scheme for Primitive Cells Figure 14.8

21. Early forms of chemolithotrophic metabolismwould have supported production of large amounts of organic compounds • Organic material provided abundant, diverse, and continually renewed source of reduced organic carbon, stimulating evolution of various chemoorganotrophic metabolisms

22. 14.3 Microbial Diversification • Molecular evidence suggests ancestors of Bacteria and Archaea diverged ~ 4 billion years ago • As lineages diverged, distinct metabolisms developed • Development of oxygenic photosynthesisdramatically changed course of evolution

23. ~ 2.7 billion years ago, cyanobacterial lineages developed a photosystem that could use H2O instead of H2S, generating O2 • By 2.4 billion years ago, O2 concentrations raised to 1 part per million; initiation of the great oxidation event • O2 could not accumulate until it reacted with abundant reduced materials (i.e., FeS, FeS2) in the oceans • Banded iron formations: iron oxides (e.g. Fe2O3) in laminated sedimentary rocks; prominent feature in geological record

24. Banded Iron Formations Iron oxides Figure 14.9

25. Development of oxic atmosphere led to evolution of new metabolic pathways that yielded more energy than anaerobic metabolisms • Oxygen also spurred evolution of organelle-containing eukaryotic microorganisms • Oldest eukaryotic microfossils ~ 2 billion years old • Fossils of multicellular and more complex eukaryotes are found in rocks 1.9 to 1.4 billion years old

26. Consequence of O2 for the evolution of life • Formation of ozone layer that provides a barrier against UV radiation • Without this ozone shield, life would only have continued beneath ocean surface and in protected terrestrial environments

27. 14.4 Endosymbiotic Origin of Eukaryotes • Endosymbiosis • Well-supported hypothesis for origin of eukaryotic cells • Contends that mitochondria and chloroplasts arose from symbiotic association of prokaryotes within another type of cell

28. Two hypotheses exist to explain the formation of the eukaryotic cell 1) Eukaryotes began as nucleus-bearing lineage that later acquired mitochondria and chloroplasts by endosymbiosis

29. 2) Eukaryotic cell arose from intracellular association between O2-consuming bacterium (the symbiont), which gave rise to mitochondria, and an archaean host

30. Both hypotheses suggest eukaryotic cell is chimeric • This is supported by several features • Eukaryotes have similar lipids and energy metabolisms to Bacteria • Eukaryotes have transcription and translational machinery most similar to Archaea

31. Major Features Grouping Bacteria or Archaea with Eukarya Table 14.1

32. II. Microbial Evolution • 14.5 The Evolutionary Process • 14.6 Evolutionary Analysis: Theoretical Aspects • 14.7 Evolutionary Analysis: Analytical Methods • 14.8 Microbial Phylogeny • 14.9 Applications of SSU rRNA Phylogenetic Methods

33. 14.5 The Evolutionary Process • Mutations • Changes in the nucleotide sequence of an organism’s genome • Occur because of errors in the fidelity of replication, UV radiation, and other factors • Adaptative mutations improve fitness of an organism, increasing its survival • Other genetic changes include gene duplication, horizontal gene transfer, and gene loss

34. 14.6 Evolutionary Analysis: Theoretical Aspects • Phylogeny • Evolutionary history of a group of organisms • Inferred indirectly from nucleotide sequence data • Molecular clocks (chronometers) • Certain genes and proteins that are measures of evolutionary change • Major assumptions of this approach are that nucleotide changes occur at a constant rate, are generally neutral, and random

35. The most widely used molecular clocks are small subunit ribosomal RNA (SSU rRNA) genes • Found in all domains of life • 16S rRNA in prokaryotes and 18S rRNA in eukaryotes • Functionally constant • Sufficiently conserved (change slowly) • Sufficient length

36. Ribosomal RNA 16S rRNA from E. coli Figure 14.11

37. Carl Woese • Pioneered the use of SSU rRNA for phylogenetic studies in 1970s • Established the presence of three domains of life: • Bacteria, Archaea, and Eukarya • Provided a unified phylogenetic framework for bacteria

38. The ribosomal database project (RDP) • A large collection of rRNA sequences • Currently contains > 409,000 sequences • Provides a variety of analytical programs

39. 14.7 Evolutionary Analysis: Analytical Methods • Comparative rRNA sequencing is a routine procedure that involves • Amplification of the gene encoding SSU rRNA • Sequencing of the amplified gene • Analysis of sequence in reference to other sequences

40. PCR-Amplification of the 16S rRNA Gene Figure 14.12

41. General PCR Protocol

42. The first step in sequence analysis involves aligning the sequence of interest with sequences from homologous (orthologous) genes from other strains or species

43. Alignment of DNA Sequences Figure 14.13

44. BLAST (basic local alignment search tool) • Web-based tool of the National Institutes of Health • Aligns query sequences with those in GenBank database • Helpful in identifying gene sequences

45. Phylogenetic Tree • Graphic illustration of the relationships among sequences • Composed of nodes and branches • Branches define the order of descent and ancestry of the nodes • Branch length represents the number of changes that have occurred along that branch

46. Phylogenetic Trees: Unrooted (a) and Rooted (b-d) Forms Figure 14.14

47. Evolutionary analysis uses character-state methods (cladistics) for tree reconstruction • The higher the proportion of characteristics that two organisms share, the more recently they diverged from a common ancestor • Cladistic methods • Define phylogenetic relationships by examining changes in nucleotides at individual positions in the sequence • Use those characters that are phylogenetically informative and define monophyletic groups (a group which contains all the descendants of a common ancestor; a clade)

48. Identification of Phylogenetically Informative Sites Dots: neutral sites. Arrows: phylogenetically informative sites, varying in at least two of the sequences. Figure 14.15

49. Common cladistic methods • Parsimony • Maximum likelihood • Bayesian analysis

50. 14.8 Microbial Phylogeny • The universal phylogenetic tree based on SSU rRNA genes is a genealogy of all life on Earth