Lecture: Archaeal diversity Dr Mike Dyall-Smith Haloarchaea Research Lab., Lab 3.07 mlds@unimelb.edu.au Reference: Microbiology (Prescott et al., 6th). Chapter 20. Archaea: Main points Discovery of a third Domain of cellular life? What are Archaea? distinguishing features, main groups, diversity Extremophiles - but not all What do they tell us about the origin and the limits of life? Life as we knew it before 1977 Archaea: Discovery Carl Woese and George Fox, 1977 Used ribosomal RNA sequences to classify organisms Surveyed many different cell types organisms grouped mainly by phenotype Discovered a new prokaryotic cell lineage (originally called archaebacteria) Discovery of the Archaea Archaea: Discovery I asked about the results. Woese was puzzled, for the pattern was unlike any he had seen; he could only conclude that: "Somehow we must have isolated the wrong RNA." So the experiment was repeated with special care, and this time, his response was: "Wolfe, these methanogens are not bacteria." "Of course they are Carl; they look like bacteria." "They are not related to any bacteria I ve seen." Because Woese had spent nearly 10 years alone developing the method, he was easily able to discern that methanogens were different! But what should the group be called? Carl Woese, Ralph Wolfe, Otto Kandler Celebrating the first conference on Archaea, (Munich, 1981) by climbing a mountain! From The Prokaryotes, R. Wolfe, 2002 From The Prokaryotes, R. Wolfe, 2002 1
Archaea: Discovery Archaea: rrna sequences used to classify cell types Ribosomal RNA (eg. 16S rrna) is highly conserved in sequence across all cells (~70%) Present in all cells (essential for translation of mrna) Allows quantitative comparisons (% differences) and evolutionary tree reconstructions. Easy to do (only about 1500 nt) Current classification of Archaea DOMAIN ARCHAEA Divided into 4 PHYLA EURYARCHAEOTA CRENARCHAEOTA KORARCHAEOTA NANOARCHAEOTA Archaea: Main points Discovery of a kingdom? What are Archaea? distinguishing features, main groups Extremophiles - but not all What do they tell us about the origin and resilience of life? 1. Prokaryotes - cell structure like Bacteria, haploid, but.. 2. Ribosomal RNA sequences show the Archaea to be related, but differ from Bacteria and Eukarya 3. Isoprenoid, ether-linked, membrane lipids (compared to ester linked lipids of Bacteria and Eukarya) 2
4. Cell wall has no murein. (various wall types; often just a protein surface layer) 5. RNA polymerase - simpler version of eukaryal RNA polymerase II 1. Prokaryotic cell structure Ribosome-packed cytoplasm Simple structure with no membranebound organelles 6. DNA genome sequences (information processing genes) Pyrolobus, showing an S-layer just outside the cytoplasmic membrane. 3. Isoprenoid membrane lipids 3. Isoprenoid membrane lipids Phospholipid cell membranes but basic structure of archaeal lipids is very different to lipids of Eukarya or Bacteria! Lipids are ether-linked, isoprenoids, not ester-linked fatty acids. Archaeol Ether bonds are more stable to heat and ph than ester bonds. Archaeol ether-linked, isoprenoids, not ester-linked fatty acids. In thermophilic archaea the phytanyl lipid can be covalently joined to another phytanyl, to form one long lipid chain. The membranes in thermophiles are often phospholipid monolayers. This makes the membranes more stable to heat. 3
4. Cell Wall structure Archaea have NO murein containing cell walls Never contains murein/peptidoglycan No D-amino acids (only L-aa) 3 main types of structure: S-layer (surface-layer) of protein Polysaccharide Murein Pseudopeptidoglycan Many Archaea have a single layer of protein outside the cell membrane. This is called a surface layer, or just S-layer. Pyrolobus, showing an S-layer just outside the cytoplasmic membrane. Archaea: Main points Discovery of a kingdom? What are Archaea? distinguishing features, main groups Extremophiles - yes, but not all What do they tell us about the origin and resilience of life? Archaea: diverse group with many extremophiles Originally 3 major (phenotypic) groups Extreme Thermophiles Extreme Halophiles Methanogens (produce methane, CH 4 ) Diverse habitats - (still finding more!) Diverse metabolisms - (not fully analysed) 4
Class III. Halobacteria: Extreme halophiles. A saltern, Geelong. Salt is piled up before being processed for sale. Crystallisation ponds in foreground. Light microscopy Class Halobacteria. Extreme Halophiles Haloferax Halobacterium Halorubrum coriense Class Halobacteria Square haloarchaea - finally cultured! Haloferax volcanii Disc shaped, S-layer Requires above 1.5M salt Aerobic heterotroph Dead Sea, Salt lakes Halobacterium salinarum - isolated from salt lakes, salted hides, salted fish, fish sauce - has bacteriorhodopsin, a photopigment that is similar to the rhodopsin of our eyes. Used for energy production. Burns et al., 2004 5
Square haloarchaea - finally cultured! Haloarcula hispanica virus His1 74 x 44 nm Burns et al., 2004 Negative stain EM, uranyl acetate Methanogens (3 Classes) Strict anaerobes (killed by oxygen) Derive energy by converting CO 2 and H 2 (or formate, methanol, acetate) to methane, CH 4 Methanogens Strict anaerobes (killed by oxygen) Autotrophic when growing on CO 2 Many genera, environmental niches eg. Muds, ruminant guts, thermophiles Methane: good fuel, greenhouse gas! Anaerobic glove box for handling and culturing methanogens Archaea: Extreme thermophiles Extreme thermophiles Access to solfatar by helicopter Hot springs and geysers. Water temperatures around 100 o C Glass slide left for a few weeks in hot water, showing bacterial growth 6
Archaea: Hyperthermophiles Archaea: Hyperthermophiles Hyperthermophiles (> 90 o C) For > 100 o C you need to go to a high pressure environment, like the deep ocean, where water pressures allow water to remain liquid well above 100 o C What places in the deep ocean are hot? Hydrothermal vents Archaea: Hyperthermophiles Submarine ALVIN Archaea: Extremophiles Black smoker or hydrothermal vent Vent fauna: clams, tube worms, crabs (above) Light microscopy (below) Electron microscopy Methanopyrus Grows at 110 o C Methanogen (produces methane) Anaerobic Isolated from hydrothermal vents Phylum Crenarchaeota: Pyrolobus Growth at 113 o C (no growth below 90 o C) Isolated from hydrothermal vents ~Coccoid shape Cell wall is a single protein layer, or S-layer. Chemolithoautotroph Oxidises H 2 for energy Thin-section electron microscopy. 7
Phylum Crenarchaeota: Pyrolobus Energy from inorganic redox reactions, ie. oxidizes H 2 and reduces nitrate Carbon from CO 2 ie. autotrophic Archaea: Main points Discovery of a new Domain of cellular life. What are Archaea? distinguishing features, main groups Extremophiles - but not all What do they tell us about the origin and resilience of life? What do Archaea tell us about life on earth? Unexpected diversity and a missing link in the evolution of the complex eukaryotic cell. Amazing limits to cellular life. Could have flourished very early after the formation of the Earth, in hot temperatures Many Archaea are lithoautotrophic, using H 2 as the electron donor and nitrate, sulfur or ferric ions as electron acceptors, and using CO 2 for their carbon. These are widespread. Widely dispersed - surface, deep ocean, and rock strata Earliest branching organisms are thermophilic What do Archaea tell us about life elswhere? Using our own example of life, all you probably need is: liquid water, a source of energy, supply of C,N,H,O,P (and a few other minerals, in low amounts) and a temperature less than about 130 o C (a guess) Mars Archaea: summary Read the chapter on Archaea in your textbook Know the distinguishing features of Archaea (compared to Bacteria and Eukarya) Know how they were discovered (16S rrna sequences) Know the names of the four Phyla Be able to describe one example from each of the 3 main phenotypic groups (extreme halophile, thermophile, methanogen) 8