1. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1 Chapter 17 Microbial Taxonomy and the Evolution of Diversity

2. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 2 Introduction to Microbial Taxonomy taxonomy –science of biological classification –consists of three separate but interrelated parts classification – arrangement of organisms into groups (taxa; s., taxon) nomenclature – assignment of names to taxa identification – determination of taxon to which an isolate belongs

3. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 3 Natural Classification arranges organisms into groups whose members share many characteristics first such classification in 18 th century developed by Linnaeus –based on anatomical characteristics this approach to classification does not necessarily provide information on evolutionary relatedness

4. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 4 Polyphasic Taxonomy used to determine the genus and species of a newly discovered prokaryote incorporates information from genetic, phenotypic, and phylogenetic analysis

5. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 5 Phenetic Classification groups organisms together based on mutual similarity of phenotypes can reveal evolutionary relationships, but not dependent on phylogenetic analysis –i.e., doesn’t weigh characters best systems compare as many attributes as possible

6. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 6 Phylogenetic Classification also called phyletic classification systems phylogeny –evolutionary development of a species usually based on direct comparison of genetic material and gene products –Woese and Fox proposed using small subunit (16S or 18S SSU) rRNA nucleotide sequences to assess evolutionary relatedness of organisms

7. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 7 Genotypic Classification comparison of genetic similarity between organisms –individual genes or whole genomes can be compared –70% homologous belong to the same species

8. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 8 Taxonomic Ranks - 1 microbes are placed in hierarchical (a system of ranking and organizing thing)taxonomic levels with each level or rank sharing a common set of specific features highest rank is domain –Bacteria and Archaea – microbes only –Eukarya – microbes and macroorganisms within domain –phylum, class, order, family, genus, species epithet, some microbes have subspecies

9. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 9 Figure 17.1

10. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 10 Species definition –collection of strains that share many stable properties and differ significantly from other groups of strains also suggested as a definition of species –collection of organisms that share the same sequences in their core housekeeping genes

11. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 11 Strains descended from a single, pure microbial culture vary from each other in many ways –biovars – differ biochemically and physiologically –morphovars – differ morphologically –serovars – differ in antigenic properties

12. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 12 Type Strain usually one of first strains of a species studied often most fully characterized not necessarily most representative member of species

13. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 13 Genus well-defined group of one or more strains clearly separate from other genera often disagreement among taxonomists about the assignment of a specific species to a genus

14. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 14 Binomial System of Nomenclature devised by Carl von Linné (Carolus Linnaeus) each organism has two names –genus name – italicized and capitalized (e.g., Escherichia) –species epithet – italicized but not capitalized (e.g., coli) can be abbreviated after first use (e.g., E. coli) a new species cannot be recognized until it has been published in the International Journal of Systematic and Evolutionary Microbiology

15. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 15 Techniques for Determining Microbial Taxonomy and Phylogeny classical characteristics –morphological –physiological –biochemical –ecological –genetic

16. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 16 Table 17.1

17. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 17 Table 17.2

18. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 18 Ecological Characteristics life-cycle patterns symbiotic relationships ability to cause disease habitat preferences growth requirements

19. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 19 Molecular Approaches extremely important because almost no fossil record was left by microbes allows for the collection of a large and accurate data set from many organisms phylogenetic inferences based on these provide the best analysis of microbial evolution currently available

20. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 20 Molecular Characteristics nucleic acid base composition nucleic acid hybridization nucleic acid sequencing genomic fingerprinting amino acid sequencing

21. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 21 Nucleic Acid Base Composition G + C content –Mol% G + C = (G + C/G + C + A + T)100 –usually determined from melting temperature (T m ) –variation within a genus usually <10%

22. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 22 Figure 17.2

23. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 23 Nucleic Acid Hybridization DNA-DNA hybridization –measure of sequence homology common procedure –bind nonradioactive DNA to nitrocellulose filter –incubate filter with radioactive single- stranded DNA –measure amount of radioactive DNA attached to filter

24. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 24 Table 17.4

25. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 25 Nucleic Acid Sequencing Small subunit rRNAs (SSU rRNAs) –sequences of 16S and 18S rRNA most powerful and direct method for inferring microbial phylogenies and making taxonomic assignments at genus level

26. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 26 Comparative Analysis of 16S rRNA Sequences oligonucleotide signature sequences found –short conserved sequences specific for a phylogenetically defined group of organisms either complete or, more often, specific rRNA fragments can be compared when comparing rRNA sequences between 2 organisms, their relatedness is represented by percent sequence homology –70% is cutoff value for species definition

27. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 27 Figure 17.3

28. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 28 Genomic Fingerprinting used for microbial classification and determination of phylogenetic relationships requires analysis of genes that evolve more quickly than rRNA encoding genes –multilocus sequence analysis (MSLA) the sequencing and comparison of 5 to 7 housekeeping genes is done to prevent misleading results from analysis of one gene used for more heterogeneous collection of microbes –multilocus sequence typing (MLST) discriminates among strains used for same pathogenic species

29. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 29 Restriction Fragment Length Polymorphism (RFLP) uses restriction enzymes to recognize specific nucleotide sequences –cleavage patterns are compared ribotyping –similarity between rRNA genes is determined by RFLP rather than sequencing

30. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 30 Figure 17.4

31. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 31 Single Nucleotide Polymorphism (SNP) Originally was designed for human Looks at single nucleotide changes, or polymorphisms, in specific genes 16S rRNA focuses on one specific gene Regions targeted because they are normally conserved, so single changes in a base pair reveal evolutionary change Distinguish between strains of B. anthracsis ( 탄저병균 ) and M. tuberculosis ( 결핵균 )

32. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 32 Figure 17.5

33. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 33 Amino Acid Sequencing amino acid sequences reflect mRNA sequence and therefore of the gene which encodes that protein amino acid sequencing of proteins such as cytochromes, histones, and heat-shock proteins has provided relevant taxonomic and phylogenetic information cannot be used for all proteins because sequences of proteins with different functions often change at different rates

34. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 34 Figure 17.6

35. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 35 Phylogenetic Trees show inferred evolutionary relationships in the form of multiple branching lineages connected by nodes identified sequences at tip of branches –operational taxonomic unit nodes represent a divergence event length of branch represents number of molecular changes between two nodes

36. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 36 Figure 17.7 considering mutation

37. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 37 Creating Phylogenetic Trees from Molecular Data align sequences determine number of positions that are different express difference –e.g., evolutionary distance use measure of difference to create tree –organisms clustered based on relatedness –assuming that the methods include maximum parsimony, meaning the fewest changes exist from ancestor to organism in question

38. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 38 Phylogenetic Trees rooted tree –has node that serves as common ancestor unrooted tree –represents a phylogenetic relationship but does not provide an evolutionary path

39. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 39 Figure 17.8

40. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 40 Phylogenetic Trees extensive horizontal gene transfer has occurred within and between domains pattern of microbial evolution is not as linear and treelike as once thought some trees attempt to display HGT –resemble web or network with many lateral branches linking various trunks –each branch representing the transfer of one or a few genes

41. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 41 Figure 17.9

42. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 42 Evolutionary Processes and the Concept of a Microbial Species

43. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 43 Evolution of the Three Domains of Life hypothesized that when RNA became enclosed in a lipid sphere, the first primitive life forms were generated last universal common ancestor (LUCA) –the root of the tree of life, based on SSU rRNA, shows the earliest region is on the bacterial branch –thought that Archaea and Eukarya evolved independently of Bacteria

44. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 44 Figure 17.10

45. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 45 Table 17.5

46. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 46 Steps in Endosymbiotic Hypothesis ancestral eukaryotic cell had lost cell wall engulfment of an endosymbiote occurred –produced needed product such as ATP genome reduction occurred evolution of organelles –mitochondria –hydrogenosome –chloroplasts

47. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 47 Mitochondria and Chloroplasts believed to be descended from Rickettsiae and Prochlorococcus –became engulfed in a precursor cell –provided essential function for host engulfed organism thought to be aerobic, thereby eliminating oxygen toxicity to the host cell host provided nutrients and a safe environment for engulfed organism

48. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 48 Hydrogenosomes asserts that the  proteobacterium endosymbiont was an anaerobic bacterium that produced H 2 and CO 2 as fermentation end products –hosts lacking external H 2 source became dependent on endosymbiont which made ATP by substrate level phosphorylation –symbiont ultimately evolved into a mitochondrion or a hydrogenosome organelle found in protists that produce ATP by fermentation

49. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 49 Eukaryotic Nucleus Evolution hypothesis 1 –archaean and bacterium living in close association (symbiosis) fused –evolution of organelles included nucleus hypothesis 2 –endosymbiosis – archaean engulfs bacterium –nucleus, mitochondria, chloroplast evolve

50. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 50 Figure 17.11

51. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 51 The Map and Definition of a Microbial Species can’t use species definition based on interbreeding because bacteria and archaea are asexual “gold standard” for species assignment may not be applicable for microorganisms

52. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 52 Microbial Evolutionary Processes Bacteria and Archaea are asexual heritable changes occur –mutation and natural selection –gene loss or gain –intragenomic recombination –horizontal gene transfer (HGT) not as important for initial evolution

53. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 53 Figure 17.12

54. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 54 Anagenesis Model of Microbial Diversity Anagenesis : genetic drift, small random genetic changes that occurs over generation microevolution –also known as genetic drift small, random genetic changes over generations which slowly drive either speciation or extinction, both of which are forms of macroevolution –only adaptive mutants are selected

55. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 55 Metapopulation Model for Microbial Diversity groups of microbes live in separate patches that represent slightly different niches population in one patch diversifies into heterogenous group scarce resources cause mingling between different patches genetic divergence occurs

56. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 56 Ecotype Model for Microbial Diversity genetically similar population of microbes is ecologically distinct members of specific ecosystem diversify and gain adaptive mutation to compete for resources extinction occurs in other ecosystems and reduced genetic variation punctuated equilibria: Evolution is periodically interrupted by rapid bursts of speciation driven by abrupt changes in the environment.

57. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 57 Horizontal Gene Transfer Model for Microbial Diversity pan-genome is complete gene repertoire of a taxon –includes the core genome plus “housekeeping” and dispensable genes –pan-genome genes acquired through horizontal gene transfer –requires genetically heterogeneous group of microbes

58. 58 Figure 17.13

59. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 59 Bergey’s Manual of Systematic Bacteriology accepted system of bacterial taxonomy detailed work containing descriptions of all bacterial species currently identified

60. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 60 The First Edition of Bergey’s Manual of Systematic Bacteriology published in 1984 and is currently in its ninth edition it contained descriptions of all known prokaryotic species

61. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 61 The Second Edition of Bergey’s Manual of Systematic Bacteriology largely phylogenetic rather than phenetic prokaryotes are divided between two domains

62. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 62 Table 17.6