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BB10B Introductory Microbiology ‘Molecular Microbial Systematics’

BB10B Introductory Microbiology ‘Molecular Microbial Systematics’. Lecture 1 Thursday 19 th Feb 8am Phylogenetics, tree of life, nomenclature Lecture 2 Friday 20 th Feb 9am Metabolic diversity Lecture 3 Tuesday 24 th Feb 9am Domain bacteria Lecture 4 Thursday 26th Feb 8am

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BB10B Introductory Microbiology ‘Molecular Microbial Systematics’

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  1. BB10B Introductory Microbiology ‘Molecular Microbial Systematics’

  2. Lecture 1 Thursday 19th Feb 8am Phylogenetics, tree of life, nomenclature Lecture 2 Friday 20th Feb 9am Metabolic diversity Lecture 3 Tuesday 24th Feb 9am Domain bacteria Lecture 4 Thursday 26th Feb 8am Domain Archebacteria

  3. Molecular Evolutionary Chronometers. 16S/18S rRNA ia a functionally related molecules in all living organisms. The genes which encode the 16SRNA molecule can be isolated from any organism. It performs the same function in all organisms. Computers are used to compare the sequences. The more different a sequencethe greater the evolutionary distance.

  4. This study of evolutionary relationships between organisms is called phylogeny and using mol boil technology is called phylogenetics. Stages in phylogenetic analysis

  5. Taxononmy looks at how organisms appear. How bacteria appear is not always useful at detecting genetic relatedness. Looking at genes allows one to get an accurate measure of how genetically similar different organisms are. We now use taxonomy to identify microorganisms. Phylogenetics to classify microorganisms.

  6. 16S RNA is the best universal chronometer. Ribosmes contain Protein and RNA. There are 3 RNA molecules. 5S, 16S and 23S (Sedimentation). Large bacterial RNA’s 16S and 23S are 1500 and 2900 nucleotides long. They both have highly conserved regions which allow the molecules to be aligned and regions of seq. variability that allow phylogenetic analysis. 5S has been used (~120bp) but it is of limited use. The 16S subunit is more experimentally manageable. It has been used to develop phylogeny’s between prokaryotes and the 18S Eukaryotic counterpart.

  7. The tree of life

  8. Eukaryote, prokaryote what is the difference? It is thought that multicelluar eukaryotes evolved from single celled eukaryotes. Single celled eukaryotes are closer to the root than multicellular This is supported by the tree. Archaea are closer to eukaryotes than bacteria. Proteobacteria is a taxonomically very diverse group, that phylogenetics shows are all related.

  9. Can also isolate DNA from a mixed culture of DNA of DNA in the environment (eg soil, around a thermal vent). Use PCR to amplify the 16S rRNA. PCR can amplify from very low levels of DNA. 2nd advantage of using PCR is that between 90 –99% of bacteria in a particular environment are not culturable. So you can amplify rRNA from bacteria that you can’t culture and get information on their classification.

  10. The tree of Life

  11. Community analysis

  12. What is a bacterial species? Plants and animals a species is defined as a population of individuals that can interbreed (under normal conditions). But for haploid prokaryotes this has no meaning. They can of course rapidly evolve. To define species it is normal to turn to molecular biological methods.

  13. A species is one that is defined as one whose 16S RNA differs by more than 3% to all other organisms should be considered a new species. A new species will be defined by characterisation of a number of strains or clones (define). Groups of species are collected into genera (single genus). Molecular criteria for a genus is 16S identity of 93-95%. Genera into Familes into orders into classes into domain.

  14. Nomenclature The naming of bacteria follows the binomial system. Names are based on latin or greek names and describe some property of the bacteria. Genus name is first, followed by species name. eg bacillus subtilis, bacillus stearothermophilus.

  15. When a new organism is discovered decisions are made as to whether it is a new species or even in a new genera. A description of the isolate is made and a pure culture deposited with an approved culture collection (eg ATCC, PCC). This becomes the standard train for that species. They are preserved live by freezing or freeze drying. It is normal for a new species description to be published in IJSB or at least a report deposited there for it to be accepted. There is no recognised list of organisms. Bergey’s Manual of Systematic Biology is taken as the best compendium. The 3rd edition should have appeared in 2000. There is a summary of the contents of the 2nd in Brock 9th ed. It is not organised phylogenetically. It is used by microbiologists to aid in identification, classification of organisms.

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