Microbial Diversity and Assessment (II) Spring, 2007 Guangyi Wang, Ph.D. POST103B

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1 Microbial Diversity and Assessment (II) Spring, 007 Guangyi Wang, Ph.D. POST03B

2 General introduction and overview Taxonomy [Greek taxis, arrangement or order, and nonos, law, or nemein, to distribute or govern]-the science of biological classification. Three interrelated parts: classification, nomenclature, & identification. classification - arrangement of organisms into groups or based on mutual similarity or evolutionary relatedness. Nomenclature - the branch of taxonomy concerned with the assignment of names to taxonomic groups according to the published rules. identification the practical side of taxonomy, the process of determining that a particular isolate belongs to a recognized taxon.

3 Why should we care about taxonomy? Easy to organize huge amount of knowledge about (micro)organisms. To make predictions and fame hypotheses for further research based on knowledge of similar organism (animal research and human health?) Places microorganism in meaningful, useful groups with precise names so that microbiologists can work with them and communicate efficiently. Essential for accurate identification of microorganisms (clinical microbiology?). It closely related to ecology, epidemiology and other scientific disciplines.

4 Two Different Possible Goals () Convenient ordering scheme. Use of a "key" Phenetic system: groups organisms based on mutual similarity of phenotypic characteristics. May or may not correctly match evolutionary grouping. Example: Group flagellated (motile) organisms in one group, non-motile organisms in another group. () Scheme displaying evolutionary relationships. Phylogenetic system: groups organisms based on shared evolutionary heritage. Example: Mycoplasma (no wall) and Bacillus (walled Gram+ rods) are not obviously similar, would not be grouped together phenetically. But evolutionarily they are similar, more so than either to Gram- organisms

5 Terminology Strain: descended from a single organism different isolates may be same species but are different strains; often have slight differences Type strain: the first strain isolated or best characterized kept in collections; e.g., ATCC (American Type Culture Collection) maintains the following frozen or freeze-dried stocks: (number of species in parentheses) Algae (0); Bacteria (4400); Fungi (000); Yeasts (4300); Protozoa (090); Cell lines: animal (300); Cell lines: plant (5); Viruses: animal (350); Viruses: plant (590); Viruses: bacteria (400)

6 many similar strains = species strain, species, genus, family, order, class, division, kingdom Example: Genus: Escherichia Species: coli Family: Enterobacteriaceae Class: Scotobacteria Division: Gracilicutes Kingdom: Procaryotae

7 Classical Taxonomy Phenetic systems (natural classification system): group organisms together based on the mutual similarity of the phenotypic characteristics. Major characteristics used in classical taxonomy: Classical characteristics: morphological characteristics, physiological and metabolic characteristics, ecologic characteristics; genetic analysis.

8 Classification of bacterial based on metabolism Bacterial metabolism is exceptionally diverse. Many chemical substrates can serve as a source of energy for bacterial growth and production. Chemosynthesis (by bacteria) is generally not as important as photosynthesis in producing organic matter, but is clearly important in understanding elemental cycling in the oceans.

9 Molecular Taxonomy Basic assumptions Genes mutate randomly Many mutations are "neutral" -- do not lead to any obvious disadvantage to the strain. Once a mutation is established, all progeny of parent cell carry that particular mutation. For example, in figure below, if template "A" is erroneously replicated to a "C" in the opposite strand instead of T, then one generation later the error will be "locked into place", and all progeny with that DNA will be forever altered (unless a reversion mutation occurs at some later time).

10 Two organisms that differ by only a few bases have diverged more recently in evolutionary time than organisms that differ by more bases. The following example shows how an evolutionary tree is constructed for four hypothetical organisms whose DNA sequence in one homologous region is known. Organism A and B differ by one base substitution. C and D also differ by one base substitution. But A and C differ by three substitutions, and A and D by four. B and C differ by three substitutions, and B and D also by four. In terms of evolutionary history, A and B appear to be very similar,as do C and D. A-B and C-D are more distantly related.

11 Computers excel at taking such data and creating trees that accurately illustrate the divergence between different organisms, with linear distance being proportional to the number of accumulated errors. Here are a couple of ways a computer could represent the separation between these four organisms:

12 Goals of molecular phylogeny Phylogeny can answer questions such as: How many genes are related to my favorite gene? Was the extinct quagga more like a zebra or a horse? Was Darwin correct that humans are closest to chimps and gorillas? How related are whales, dolphins & porpoises to cows? Where and when did HIV originate? What is the history of life on earth?

13 Was the quagga (now extinct) more like a zebra or a horse?

14 Woese PNAS

15 Molecular phylogeny: nomenclature of trees There are two main kinds of information inherent to any tree: topology and branch lengths. We will now describe the parts of a tree.

16 A B C D E F G H I time 6 6 A B C D E one unit Molecular phylogeny uses trees to depict evolutionary relationships among organisms. These trees are based upon DNA and protein sequence data.

17 Tree nomenclature taxon taxon I G F H 6 A B C D 6 B D A C time E one unit E

18 Tree nomenclature operational taxonomic unit (OTU) such as a protein sequence taxon I G F H 6 A B C D 6 B D A C time E one unit E OUT-One of the organisms being compared in a phylogenetic analysis.

19 Tree nomenclature branch (edge) I G Node (intersection or terminating point of two or more branches) 6 F H A B C D 6 B D A C time E one unit E

20 Tree nomenclature Branches are unscaled... Branches are scaled... I G F H 6 A B C D 6 B D A C time OTUs are neatly aligned, and nodes reflect time E one unit branch lengths are proportional to number of amino acid changes E

21 Tree nomenclature bifurcating internal node multifurcating internal node I G F H 6 A B C D 6 B D A C time E one unit E

22 Tree nomenclature: clades Clade ABF (monophyletic group) I G F H 6 time A B C D E ) Monophyletic group is applied to a group of organisms that includes an ancestral species and all of its descendants; e.g. Aves, Mammalia. This group is a complete branch of the tree of life, the phylogeny of life. Such a branch is called a clade. ) The Polyphyletic taxon is a group composed of a number of organisms which might bear some similarities, but does not include the most recent common ancestor of all the member organisms (usually because that ancestor lacks some or all of the characteristics of the group). The taxon shares derived characters which originated several times by convergence.

23 Tree nomenclature I G F H 6 A B C D Clade CDH E time Fig..4 Page 366

24 Tree nomenclature Clade ABF/CDH/G I G F H A B C 6 D E time Fig..4 Page 366

25 Examples of clades Lindblad-Toh et al., Nature 438: 803, 8 Dec. 005, fig. 0

26 Tree roots The root of a phylogenetic tree represents the common ancestor of the sequences. Some trees are unrooted, and thus do not specify the common ancestor. A tree can be rooted using an outgroup (that is, a taxon known to be distantly related from all other OTUs).

27 Tree nomenclature: roots past present Rooted tree (specifies evolutionary path) Unrooted tree Fig..6 Page 368

28 Tree nomenclature: outgroup rooting past 9 0 root present 3 4 Rooted tree Outgroup (used to place the root) Fig..6 Page 368

29 Requirements for Molecular clock Attempt to use basic assumptions to establish history of evolutionary lineages Over long periods of time, assume mutations occur with roughly predictable frequency Universally distributed across the group chosen for study Functionally homologous in each organism or with identical function Properly align the two molecules in order to identify regions of sequence homology and sequence variance. Change at a rate commensurate with the evolutionary distance measure. e.g. cytochromes, iron-sulfur proteins (ferredoxins), ATPase, RecA, & Ribosome RNA.

30 Use of 6S RNA sequence homology 6S RNA is found in small ribosomal subunit (30S) of procaryotic ribosomes. Since mitochondria and chloroplasts have these ribosomes also, it is found in all 3 kingdoms. Most ribosomal RNA mutations are deleterious. Very few mutations are neutral. Therefore evolution of 6S RNA is very slow. It is a very good molecule to use to compare organisms that may have diverged as far back as 3 or 4 billion years ago. Visit the Ribosomal Database Project on the Web for access to data and software tools. This site lets users upload sequence information, generates alignments with other ribosomal genes, and returns aligned sequences with best matches, as well as generating phylogenetic trees.

31 Three Domains of Life CLASSIFICATION - 3 Domains (Woese, 978): Current Eubacteria - true bacteria Archaebacteria - ancient bacteria Eukaryotes - protists, fungi, plants, animals

32 ProKaryotes divided into two distinct groups very early on. The archaea and bacteria first diverged, the eukaryotes developed.

33

34 Phylogenetic Classifications Bergey s Manual of Systematic Bacteriology - nd ed emphasis on 6S rrna sequence phylogenetic classification Vol. Archae & Deeply Branching & Phototrophic Bacteria Vol. Proteobacteria Vol. 3 The Low G+C Gram-positive Bacteria Vol. 4 The High G+C Gram-positive Bacteria Vol. 5 The Planctomycetes, Spirochaetes, Fibrobacteria, Bacteroidetes & Fusobacteria

35 Phylogenetic Classifications Bergey s Manual of Systematic Bacteriology - nd ed

36

37 Phylogentic Overview of Bacteria Detailed phylogenetic tree of the major lineages (8 phyla) of Bacteria based on 6S ribosomal RNA sequence comparisons

38 Archaea consist of 3 distinct groups

39 Summary Importance of taxonomy Type of taxonomy Understand phylogenetic tree Main groups of bacteria

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