Phys 214. Planets and Life

1. Phys 214. Planets and Life Dr. Cristina Buzea Department of Physics Room 259 E-mail: cristi@physics.queensu.ca (Please use PHYS214 in e-mail subject) Lecture 17. Life at the extremes. Part III February 29th, 2008

2. Contents Life at the extreme – part III Acid pH Alkaline pH Radiation Subsurface rocks environments High pressure Anaerobes, methanogens Low carbon Low water activity

3. Acid pH - acidophile Extremophile in Rio Tinto, Spain, in pH = 0. The Rio Tinto is an extremely acidic river in Spain. The river is full of heavy metals. Surprisingly, phylogenetic studies show the diversity of eukaryotes to be much greater than that of prokaryotes. Lemonade Spring, Yellowstone National Park. Bright green -abundance of Cyanidium, the most heat and acid tolerant alga known. Acidophilic - organisms that thrive under highly acidic conditions (pH 2.0 or below) . Domain: Archaea, Bacteria, Eukarya (algae, Fungus). Habitat: acid springs and rivers, old mines drainage, solfataric sites

4. Acid pH - acidophile Seviche – popular latin American dish with raw fish in lime or lemon juice What happens at a high acid content to most organisms? The extent to which the water solution acts as an acid or a base (expressed as pH) is crucial to the stability of proteins as folded structures, and for the transport of ions through the cell membrane. The pH of the standard ocean environment is 8.2. Fish die at a pH less than 4. Proteins in acidic solution will denature: fish cooked in the absence of heat – seviche. Adaptation: - Keep the cytoplasm at a neutral pH - pump protons out of the intracellular space - proteins do not need to develop acid stability. - Keep the cytoplasm acidified - forces nearly all proteins evolve acid stability

5. Alkaline pH - Alkaliphiles Octopus Spring is an alkaline hot spring, located in Yellowstone National Park, that supports the growth of thermophilic bacteria. Mono Lake, located in California's Eastern Sierra, is both alkaline and hypersaline. Alkaline Lake, of the Eastern Sierras, is shown above with a soft, gelatinous microbial mat forming over the surface. Alkaliphiles - thrive in alkaline environments with a pH of 9 to 11. Domain: Eukarya, Archaea, and Bacteria Habitat: soda lakes and carbonate-rich soils. Adaptability: have evolved pH stable enzymes; they are often used in the manufacturing of detergents. compensate for reversal of the pH gradient by having a high membrane potential. Microcystis isolated from Alkaline Lake in the Eastern Sierras. Colonies of blue green alga are embedded in a mucus material. Anabaena is a filamentous blue-green algae commonly associated with alkaline lakes.

6. High Radiation - Radiotolerant Deinococcus radiodurans Radiotolerant - property of organisms capable of living in environments with very high levels of radiation. Environment: Many organisms (survival of many animals and plants around the Chernobyl accident; uranium mines in Brasil many radioresistant insects, worms and plants, scorpions). Radiation can increase the growth rate of the seeds. Surface of Earth is protected from lethal particles associated with cosmic rays. UV radiation is diminished by a layer of ozone that probably fluctuated over the last 2 billion years. Resistance to radiation discovered when experimenting food sterilization. After high doses of radiation some bacterial communities persisted.

7. High Radiation - Radiotolerant What happens to most organisms when subjected to radiation? • Photon and particle radiation damage to the cells – the most severe to the structure of the DNA • Enzymes exist to repair DNA, however if the radiation is high, exceeds the ability of enzymes to repair fast enough -> the genetic code will be corrupted • The most lethal damage is the breakage of both DNA strands • In multicellular organisms the physiological effects of exposure to radiation are complex, ranging from cataracts, sterility, cancer, death. • Some particles cause more damage than other particles, therefore counting number of particles per surface area is not a proper measure • For a given amount of energy absorbed per mass of tissue, energetic particles cause more damage than photons, and particles with higher atomic mass do more damage than particles with lower atomic mass • Units of radiation – sievert , rad – account for both rate of energy input and absorption by tissues • 100 rads = one joule of radiation input into an organism per kilogram of cells • The background dose of cosmic radiation in terrestrial environment is 0.5 rad/year • Immediately lethal dose for humans – 2,000-5,000 rads.

8. High Radiation - Radiotolerant Deinococcus radiodurans - survive extreme levels of radiation, extreme temperatures, dehydration, and exposure to genotoxic chemicals. They have the ability to repair their own DNA, usually with 48 hours. Highly resistant to lethal radiation levels; up to 1.5 million rads of radiation, a dose 3000 times higher than would kill organisms (from microbes to humans). Useful in cleaning up mixed-waste sites contaminated with toxic chemicals as well as radiation. It is one of the few life forms found in extremely dry areas. The unique defense mechanism that evolved to help it combat dehydration proves useful in protecting it from radiation. Recently discovered DNA rings in D. rad.

9. High Radiation - Radiotolerant Adaptation: 1) DNA repair Human cells, can mend only very few breaks in their DNA. D. radiodurans can fix more than 200! It was believed that it must have effective enzymes that repair DNA, but its repair enzymes are very similar to those existing in ordinary bacteria! 2) Compartments Microbe's DNA is organized in a unique ring that prevents pieces of DNA broken by radiation from floating off into the cell's liquids. (In other organisms the DNA fragments are lost). The fragments are brought back together by repair enzymes, reconstructing the DNA strands. The bacterium is composed of four compartments, each containing one copy of DNA. Two small passages between the compartments. After being repaired (1h30min), the DNA unfolds and migrates to an adjacent compartment where it mingles with the copy of DNA residing there. Then the repair enzymes (common in humans and bacteria alike) compare between the two copies of DNA, using each as a template to fix the other. Out of the four copies of DNA, there are always two or three tightly packed in a ring while the other copies are free to move about. Thus at any given moment there are copies of DNA that drive the production of proteins and others that are inactive but continuously protected.

10. High Radiation - Radiotolerant Microbes found two mile deep in rocks containing radioactive uranium, thorium, & potassium, Radioactivity breaks eater molecules into oxygen and hydrogen. Oxygen combines with water to form hydrogen peroxide (H2O2). The peroxide reacts with iron-sulfur compounds (FeS2), producing sulfate ions (SO42-) that the microbes eat. The two lacking electrons are supplied inside the organism by the leftover hydrogen gas. Subsurface microbes reproduceonce a year at most, and possibly only every 300 years … or more! E. coli found in the intestines of mammals divide every day or so. Microscopic photo of metal-oxidizing bacteria found in biofilm samples taken from a South African gold mine. NSF

11. Subsurface rocks - Endoliths Endolith lifeform found inside an Antarctic rock Courtesy of NOAA ocean explorer Adaptation: survive by feeding on traces of iron, potassium, or sulfur; very slow procreation cycle (some only engage in cell division once every hundred years). Iron oxide can react with water and produce hydrogen 2 FeO + H2O -> H2 + Fe2O3 Molecular hydrogen can be used to sustain biological processes through oxidation of hydrogen back to H2O , H2S, or other compounds. Endolith - lives inside rocks, between mineral grains or in pores. Very deep rocks - also deal with extreme temperatures, intense pressures, total darkness, and anoxic conditions. Archaea, Bacteria, fungus. Environment: Sparse eater and nutrients: in rocks down to a depth of 3 km (9,600 feet), surface rocks in regions of low humidity and low temperature, including the Dry Valleys and permafrost of Antarctica. During a study of Sweeden for long-term nuclear waste disposal, previously unknown microbial ecosystems were discovered in igneous rocks below 1,000 m. Survival limited by lack of nutrients & increased temperature -> temperature limit ~ 120°C -> limits the possible depth to 4 km below the continental crust, and 7 km below the ocean floor.

12. Nanobacteria Nanobacteria = the smallest cell-walled bacteria (belongs to Proteobacteria). 100-500nm (1/10 the size of bacteria). Does it has enough room to house necessary cell components such as DNA, RNA, and plasmids? It seems it does! Environment - within rocks and organisms, present in the upper stratosphere. Found in human blood and may be related to diseases involving biomineralization: kidney stones, tooth plaque, artery calcifications, etc.. Extremes: low and high temperatures, UV, radiation. Models predict that nanobacteria (NB) can survive extreme conditions in space by protecting themselves from desiccation with a self-synthesized slime that seals their mineral shells. It’s resistance can be associated with the layer of calcium phosphate (apatite) that nanobacteria is able to synthesize. Cultured Nanobacteria. Kajander et al.Proc. Natl. Acad. Sci. USA 95 (1998) 8274

13. Nanobacteria In the bacterial world, slime has principally one function: to establish stable bonds to surfaces encouraging the formation of complex multispecies communities (biofilms), thereby enhancing conditions for a physical contact between individuals, a precondition for horizontal gene transfer. For nanobacteria the slime provides at least three functions: • protection from desiccation • Facilitation of colony formation, offering favorable conditions for growth and replication. • a stress response, induced by a programmed survival mechanism, triggered by rapid changes in their environment. The slime synthesized by NB consists of glycoproteins - linked to primordial proteins. Nanobacteria -Probably the inhabitants of the primordial world. Nanobacteria fossils were found in Martian meteorites ALH84001 (several billion years old) (controversial). Cultured Nanobacteria. Kajander et al.Proc. Natl. Acad. Sci. USA 95 (1998) 8274 Potential fossil of a simple Martian organism that lived over 3.6 billion years ago? D. McKay (NASA /JSC), K. Thomas-Keprta (Lockheed-Martin), R. Zare (Stanford), NASA

14. High Pressure - Barophiles Barophiles (piezophile) =organisms which live in high pressure environments. Environments: on oceans floors and deep lakes (hydrostatic pressures), in subsurface rocks (lithostatic pressures) Barotolerants - able to survive at high pressures, but can exist in less extreme environments as well. Usually don't grow at pressures higher than 500 atm. Obligate barophiles (extreme)- cannot survive outside of such environments. Lithostatic pressure increases with about 2 atmosphere for every 10 meters depth. Hydrostatic pressure increases with one atmosphere for about every 10 meters. Oceans average depth = 3,800 m -> pressure of 380 atm Maximal depth = 11,000 m -> maximum pressure of 1100 atm (10 atm = 1 MPa, 1 bar = 100,000 Pa) Barophiles also tend to be psychrophilic. (Below 100m the temperature is ~ 2-3 °C). Barophiles grow in darkness -> are very UV sensitive, lacking mechanisms of DNA repair.

15. High Pressure - Barophiles What happens at high pressures? High pressure affects cell processes in similar way to low temperatures. High pressure decreases volumes and compresses cell content. A) Decreased cell membrane fluidity. B) Decreased binding capacity of enzymes C) The 3-dimensional structures of DNA and proteins distort and become nonfunctional Adaptation A1) higher percentages of (poly)unsaturated fatty acids A2) the cell wall outer membranes of barophiles tend to have a different protein composition compared to regular microbes. The porins (diffusion channels in membranes) of a barophile can be made up by a specific outer membrane protein (caused by a specific gene which is switched on by high pressure). B) The enzymes of extreme barophiles are often folded differently, in a way so that the pressure has less effect on them. High-pressure genes were found not only in deep-sea adapted microorganisms, but also in bacteria growing at atmospheric pressure -> life emerged from a deep sea environment.

16. Mariana trench - the deepest mud sample • Mariane trench - the deepest sea floor at 10,897 m. • In 1996 the Japanese submersible Kaiko scooped out some mud from the mariana trench sea floor. • Successfully isolated some 180 species of microorganisms. • Many were extreme barophiles; their growth rate much lower than barotolerant microbes. The Challenger Deep is the deepest surveyed point in the oceans - in the southern end of the Mariana Trench. Amphipods, Hirondellea gigas, shrimp-like animals were collected by baited traps. The total length of the largest specimen was over 45mm The photo shows barophilic bacteria isolated from seafloor mud of the Mariana Trench sampled by the KAIKO.

17. High Pressure - Barophiles - water Obligate barophile - bacteria which cannot proliferate at pressures lower than 500 atms., but proliferate best at 800 atms. The photo compares morphological changes of barophile bacterium and Escherichia coli. E. coli can withstand high pressures and still be viable. Under very high pressure E. coli do not proliferate well, and the cell elongates. Obligate barophiles grows better as pressure increases. Barophilic bacteria E. coli (barotolerant) 1,000 m 3,000 m 5,000 m

18. Bacteria survives trip to the Moon Interior view of Surveyor 3 TV camera; surviving microorganisms cultured from the polyurethane foam insulation. Surveyor 3 landed on the moon on April 20, 1967. Culture plate from 3 camera foam sample showing Streptococcus mitis. a common harmless bacteria from the nose, mouth& throat in humans. Streptococcus mitis - the only known survivor of unprotected space travel. It survived: • launch • space vacuum • 3 years of radiation exposure • deep-freeze at an average temperature of only 20 K • no nutrient, water or energy source A normal human has about a trillion bacteria on the skin, 10 billion in the mouth, and 100 trillion in the gastrointestinal tract. These numbers are much larger than the number of eukaryotic cells which comprise the human host.

19. Anaerobes, Methanogens Anaerobe = cannot tolerate oxygen Aerobe = requires oxygen (Homo sapiens) Methanogens All known methanogens are both archaeans and anaerobes. Environment: dry desert soils, deep subterans, wetlands, in the guts of animals (ruminants, humans) where they are responsible for flatulence. More than 50 species of methanogens identified, including a number that are extremophiles. Live methanogens were recovered from 3 km under Greenland. Some scientists have proposed that the presence of methane in the Martian atmosphere may be indicative of native methanogens on that planet. Methanogens. Credit: Maryland Astrobiology Consortium, NASA, and STScI

20. Low carbon environment Oligotroph - organism that can live in a very low carbon concentration (<one part per million). Domains:Most are bacteria, and some Archaea. Environment:Low-carbon environments are ubiquitous; most of the open ocean; deep waters, deep sediments; caves, glacial and polar ice, deep subsurface soil. Adaptation: Slow growth, low rates of metabolism, and generally low population density. Science 309 (2005) Pelagibacter ubique - the most abundant organism in the oceans - estimated 1027 . They are some of the smallest self-replicating cells known -length 600 nm, diameter 160 nm. Has one of the smallest genomes, yet it includes all of the essential genes to exist without help from other organisms.

21. Low water activity - Xerophiles Atacama desert, Andes, South America, the driest environment on Earth, analogue to Martial soil Lake Hoare in the McMurdo Dry Valleys, Canada Glacier in the background. Peter West, NSF Xerophile = organism that can grow with a low water content. Environment - dry soil, rocks, soda lake, deep-sea brines, foods with high solute content (jam, honey, dried fruit). The Antarctic Dry Valleys -a region where there is no ice present and periodically there is very little free water. This extreme ecosystem is also seen as a potential analogue for possible life on Mars. Domains: Bacteria, Archaea, Eukarya (yeasts, molds, fungi, lichens, cactus, some nematodes). Endoliths and halophiles are often xerotolerant. What happens at low water activity: Loss of water -> irreversible damage to cells

22. Amber encapsulated bacteria revived AMG-D1T growing for 48 h at 30oC showing cell division. International Journal of Systematic Bacteriology (1998), 48, 511 Dominican amber - 20-40 million years old • Two Staphylococcus-like strains, AMG-D1T and AMG-D2, which were isolated from plant and soil inclusions in Dominican amber, estimated to be 25–40 million years old. • Amber, a polymeric glass formed over time from the resins of conifers and some flowering plants, provides an excellent preservative matrix for biological specimens.

23. Next lecture Chapter 6. The origin and evolution of life on Earth