Bergey s Manual Classification Scheme. Vertical inheritance and evolutionary mechanisms

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1 Bergey s Manual Classification Scheme Gram + Gram - No wall Funny wall Vertical inheritance and evolutionary mechanisms a b c d e * * a b c d e * a b c d e a b c d e * a b c d e Accumulation of neutral mutations with time 1

2 GC ratio DNA-DNA hybridization 2

3 DNA-DNA hybridization DNA-DNA hybridization tree for enteric bacteria Limited to analysis of very close relatives 3

4 BBOM Species definition (older ed.) Of prokaryotes, a collection of closely related (>97% 16S rrna sequence homology and >70% genomic hybridization) strains sufficiently different from all other strains to be recognized as a distinct unit The concept of housekeeping genes 4

5 Microbial Classification Based primarily on 16S (or 18S) rrna gene What is rrna? Ribosome components 5

6 16S rrna Microbial Classification Based primarily on 16S (or 18S) rrna gene What is rrna? Why use rrna as a phylogenetic marker? 6

7 Interaction of 16S rrna with other components 7

8 Microbial Classification human yeast corn Escherichia coli Anacystis nidulans Thermotoga maratima Methanococcus vannielii Thermococcus celer Sulfolobus sulfotaricus...gtgccagcagccgcggtaattccagctccaatagcgtatattaaagttt......gtgccagcagccgcggtaattccagctccaatagcgtatattaaagttc......gtgccagcagccgcggtaattccagctccaatagcgtatatttaagttc......gtgccagcagccgcggtaatacggagggtgcaagcgttaatcggaattt......gtgccagcagccgcggtaatacgggagaggcaagcgttatccggaattc......gtgccagcagccgcggtaatacgtagggggcaagcgttacccggatttg......gtgccagcagccgcggtaataccgacggcccgagtggtagccactcttc......gtggcagccgccgcggtaataccggcggcccgagtggtggccgctattc......gtgtcagccgccgcggtaataccagctccgcgagtggtcggggtgattc... Microbial Classification human yeast corn Escherichia coli Anacystis nidulans Thermotoga maratima Methanococcus vannielii Thermococcus celer Sulfolobus sulfotaricus Unknown soil isolate...gtgccagcagccgcggtaattccagctccaatagcgtatattaaagttt......gtgccagcagccgcggtaattccagctccaatagcgtatattaaagttc......gtgccagcagccgcggtaattccagctccaatagcgtatatttaagttc......gtgccagcagccgcggtaatacggagggtgcaagcgttaatcggaattt......gtgccagcagccgcggtaatacgggagaggcaagcgttatccggaattc......gtgccagcagccgcggtaatacgtagggggcaagcgttacccggatttg......gtgccagcagccgcggtaataccgacggcccgagtggtagccactcttc......gtggcagccgccgcggtaataccggcggcccgagtggtggccgctattc......gtgtcagccgccgcggtaataccagctccgcgagtggtcggggtgattc......gtgtcagccgccgcggtaataccagctccgcgagtggtcggggtgattc... 8

9 Small subunit (16S) rrna PCR amplification of SSU rrna genes Focus on a particular gene in the genome 9

10 PCR amplification of SSU rrna genes Sequencing Reactions How does a ddntp terminate DNA replication? dntp ddntp 10

11 Sequencing Reactions Inside a capillary sequencer 11

12 Creating phylogenetic trees human yeast corn Escherichia coli Anacystis nidulans Thermotoga maratima Methanococcus vannielii Thermococcus celer Sulfolobus sulfotaricus...gtgccagcagccgcggtaattccagctccaatagcgtatattaaagttt......gtgccagcagccgcggtaattccagctccaatagcgtatattaaagttc......gtgccagcagccgcggtaattccagctccaatagcgtatatttaagttc......gtgccagcagccgcggtaatacggagggtgcaagcgttaatcggaattt......gtgccagcagccgcggtaatacgggagaggcaagcgttatccggaattc......gtgccagcagccgcggtaatacgtagggggcaagcgttacccggatttg......gtgccagcagccgcggtaataccgacggcccgagtggtagccactcttc......gtggcagccgccgcggtaataccggcggcccgagtggtggccgctattc......gtgtcagccgccgcggtaataccagctccgcgagtggtcggggtgattc... Unknown assignment part 1 You will conduct a BLAST search to identify your unknown for this assignment. Unknown assignment part 2 Next you will use the Ribosomal Database Project (RDP) to identify the same unknown. Worth 30 points. Due 1 week from today! 12

13 How do you read a phylogenetic tree? How do you read a phylogenetic tree? 13

14 Introduction to the bacterial Kingdoms Introduction to the bacterial Kingdoms Early branches are minor groups with few species that are not generally abundant, and they are primitive organisms (short branch length) Most of the branches (certainly most of the branches with lots of known and abundant species) radiate from a single point in the tree - main radiation Early, primitive branches: Aquifex/Hydrogenobacteria Thermotoga Green non-sulfur Bacteria Main radiation: Deinococci Spirochaetes Green sulfur Bacteria Bacteroides/Flavobacteria Planctomycetes Chlamydia Cyanobacteria Purple Bacteria Gram positive Bacteria 14