Microbes run the planet - Jonathan Eisen slides from #scifoo 2006
•Download as PPT, PDF•
0 likes•1,798 views
Presentation by Jonathan Eisen from SciFoo meeting in 2006
Recommended
Recommended
More Related Content
What's hot
What's hot (20)
Similar to Microbes run the planet - Jonathan Eisen slides from #scifoo 2006
Similar to Microbes run the planet - Jonathan Eisen slides from #scifoo 2006 (20)
More from Jonathan Eisen
More from Jonathan Eisen (20)
Recently uploaded
Recently uploaded (20)
Microbes run the planet - Jonathan Eisen slides from #scifoo 2006
- 1. Microbes Can Grow On Anything • Energy – Light – Organic and inorganic chemicals • Carbon – Organic degradation – Inorganic “fixation” • CO2, CO, CH4 • Contol global cycling of most nutrients – N, S, P, – Can manipulate just about every form
- 2. QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture.
- 3. Extremophily Type Conditions Temperature Thermophiles, Psychorphile pH Alkaliphiles, Acidiphiles Pressure Barophile Salt Halophiles Radiation Radiophiles
- 5. QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture.
- 6. How Survive at 100°C • Change amino acid composition of all proteins • Change composition of membranes • Add enzymes to repair heat specific damage (e.g., deamination of DNA) • Changing which metals are used as cofactors in biological processes • Cell wall coatings
- 7. QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture.
- 9. QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture.
- 10. How Survive at High Salt • High salt will cause water to want to flow out of cell • Compensate by increasing solute concentrations in cell • Many organisms use different solutes • Extreme halophiles fill up inside of cell with salts also • Enzymes from these organisms work well in industrial applications where salts are present
- 12. QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture.
- 13. How Survive Desiccation? • Spore formation • Increase solute concentration • Starvation tolerance • Repair desiccation damage
- 15. But ….
- 16. Great Plate Count Anomaly Culturing Microscope Count Count
- 17. Great Plate Count Anomaly Culturing Microscope Count <<<< Count
- 18. Environmental Microbiology Era I: Who is out There?
- 19. rRNA Revolution • Morphology and physiology evolve too rapidly • Molecular systematics is the only way • 16s rRNA is the choice • Three domains discovered
- 20. PCR Saves the Day
- 21. Solving the Plate Count Anomaly PCR Culturing Microscope Count Count
- 22. Compare PCR Amplified rRNA To Those of Cultured Species Eisen et al. 1992
- 23. Majority of Microbes are “Uncultured” Numbers and Diversity
- 24. Problems with rRNA PCR • Doesn’t predict biology of organisms well • Doesn’t work for viruses • Not very quantitative
- 25. Environmental Microbiology Era II: What are they Doing?
- 26. Metagenomics by Large Inserts • Isolate, by filtration, all microbes in a sample • Extract total DNA in very large pieces • Clone those pieces as BACs into E.coli to get enough. • ID BACs of interest (e.g., containing rRNA) • Sequence and analyze the BACs like a bacterial genome Sample Gene Filter Extract Clone Sequence DNA List concentrate Into BACs
- 27. Phylogenetic Anchors Beja et al. 2000
- 28. Using a rRNA anchor allowed the identification of a new form of phototrophy: Proteorhodopsin Beja et al. 2000
- 29. Beja O, et.al., Science 2000 289:1902-6, Nature (2001) 411: 786-789
- 30. Limits of Large Insert Approach • Large insert libraries less random and less representative than small inserts • Lower throughput • Requires some thinking
- 31. Enviornmental Microbiology Era III: Environmental Shotgun Sequencing
- 32. Environmental Shotgun Sequencing shotgun Warner Brothers, Inc. sequence
- 33. Assemble Fragments sequencer output assemble fragments Closure & Annotation
- 34. Baumannia cicadellinicola genome project: 1° symbionts of the Glassy-winged Sharpshooter • Sap feeding insects • Carriers of Xylella fastidiosa that causes Pierce’s disease of grapevines • There are >20000 sharpshooter species, Glassy-winged Sharpshooter within which intracellular symbiotic bacteria are wildspread
- 36. Co-Symbiosis?
- 37. Sargasso Sea Shotgun Sequencing QuickTime™ and a TIFF (LZW) decompressor shotgun are needed to see this picture. QuickTime™ and a TIFF (LZW) decompressor are needed to see this picture. sequence Analysis led by Venter Institute. Eisen lab contributions by Dongying Wu, Martin Wu, Jonathan Badger
- 38. Can Learn By “Black Box” Approach
- 39. Binning Much More Difficult in Complex Communities A T B U C V D W E X F Y G Z
- 40. rRNA Phylotypes Venter et al., 2004
- 41. taxonomic content per SHOTGUN 16S 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- S- 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23 25 26 27 28 29 30 31 32 33 34 35 36 Station
- 42. Shotgun Sequencing Allows Use of Alternative Anchors (e.g., RecA) Venter et al., 2004
- 43. Other Markers Give Similar Phylotpyes Sargasso Phylotypes 0.5 0.45 0.4 0.35 EFG 0.3 EFTu HSP70 0.25 RecA 0.2 RpoB rRNA 0.15 Weighted % of Clones 0.1 0.05 0 CFB Chlorobi Firmicutes Chloroflexi Fusobacteria Spirochaetes Cyanobacteria Actinobacteria Euryarchaeota Crenarchaeota BetaproteobacteriaDeltaproteobacteria Alphaproteobacteria Epsilonproteobacteria Gammaproteobacteria Deinococcus-Thermus Major Phylogenetic Group
- 44. Shotgun Sequencing Detects More Diversity than PCR-methods
- 45. Biased Sampling of Genomes
- 46. Biased Sampling of Genomes
- 47. Proteobacteria TM6 OS-K • At least 40 Acidobacteria Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA WS3 Gemmimonas Firmicutes Fusobacteria Actinobacteria OP9 Cyanobacteria Synergistes Deferribacteres Chrysiogenetes NKB19 Verrucomicrobia Chlamydia OP3 Planctomycetes Spriochaetes Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 OP11
- 48. Proteobacteria TM6 OS-K • At least 40 Acidobacteria Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Genome WS3 Gemmimonas Firmicutes sequences are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria three phyla Synergistes Deferribacteres Chrysiogenetes NKB19 Verrucomicrobia Chlamydia OP3 Planctomycetes Spriochaetes Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 OP11
- 49. Proteobacteria TM6 OS-K • At least 40 Acidobacteria Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Genome WS3 Gemmimonas Firmicutes sequences are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria three phyla Synergistes Deferribacteres Chrysiogenetes • Some other NKB19 Verrucomicrobia Chlamydia phyla are OP3 Planctomycetes Spriochaetes only sparsely Coprothmermobacter OP10 sampled Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 OP11
- 50. Proteobacteria TM6 OS-K • At least 40 Acidobacteria Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Genome WS3 Gemmimonas sequences are Firmicutes Fusobacteria mostly from Actinobacteria OP9 Cyanobacteria three phyla Synergistes Deferribacteres Chrysiogenetes • Some other NKB19 Verrucomicrobia Chlamydia phyla are only OP3 Planctomycetes sparsely Spriochaetes Coprothmermobacter OP10 sampled Thermomicrobia Chloroflexi TM7 • Solution: Deinococcus-Thermus Dictyoglomus Aquificae sequence more Thermudesulfobacteria Thermotogae phyla OP1 OP11
Editor's Notes
- An example of the reasons predicting function is difficult comes from our work on Deincooccus radiodurans , the most radiation resistant organism known. When TIGR sequenced the genome of this species (just before I got to TIGR) I helped look at the predicted DNA repair genes in the genome in the hope that this analysis would tell us something about this species radiation resistance. I was very interested in this since my Ph.D was on comparative studies of DNA repair, especially in extremophiles.
- Extension of rRNA analysis to uncultured organisms using PCR
- Phylogenetic analysis of rRNAs led to the discovery of archaea
- Functional prediction using a gene tree is just like predicting the biology of a species using a species tree
- This is a tree of a rRNA gene that was found on a large DNA fragment isolated from the Monterey Bay. This rRNA gene groups in a tree with genes from members of the gamma Proteobacteria a group that includes E. coli as well as many environmental bacteria. This rRNA phylotype has been found to be a dominant species in many ocean ecosystems.
- Metagenomics involves cloning large DNA fragments from environmental samples and then selecting specific fragments for further sequencing. The selection of specific fragments can be based on mapping rRNA genes to them, mapping functional genes, or by first doing end-sequencing and then selecting fragments with interesting end-sequences.
- This is a tree of a rRNA gene that was found on a large DNA fragment isolated from the Monterey Bay. This rRNA gene groups in a tree with genes from members of the gamma Proteobacteria a group that includes E. coli as well as many environmental bacteria. This rRNA phylotype has been found to be a dominant species in many ocean ecosystems.
- Metagenomic analysis led to the discovery of a new form of phototrophy in the ocean
- PCR primers designed from the metagenomic sequences were then used to discover additional forms of the proteorhodopsin that is the basis for the new form of phototrophy
- This is a tree of a rRNA gene that was found on a large DNA fragment isolated from the Monterey Bay. This rRNA gene groups in a tree with genes from members of the gamma Proteobacteria a group that includes E. coli as well as many environmental bacteria. This rRNA phylotype has been found to be a dominant species in many ocean ecosystems. clone from the Sargasso Sea. This shows that this