Transcript ppt

Phys 214. Planets and Life
Dr. Cristina Buzea
Department of Physics
Room 259
E-mail: [email protected]
(Please use PHYS214 in e-mail subject)
Lecture 17. Life at the extremes.
Part III
February 29th, 2008
Contents
Life at the extreme – part III
Acid pH
Alkaline pH
Radiation
Subsurface rocks environments
High pressure
Anaerobes, methanogens
Low carbon
Low water activity
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
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
Alkaline pH - Alkaliphiles
Alkaline Lake, of the Eastern Sierras, is
shown above with a soft, gelatinous
microbial mat forming over the surface.
Octopus Spring is an alkaline hot spring,
located in Yellowstone National Park, that
supports the growth of thermophilic bacteria.
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.
Mono Lake, located in
California's Eastern Sierra, is
both alkaline and hypersaline.
Anabaena is a filamentous bluegreen algae commonly
associated with alkaline lakes.
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.
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.
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.
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.
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 reproduce once 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
Subsurface rocks - Endoliths
Endolith lifeform found inside an Antarctic rock
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.
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.
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
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
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.
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 deepsea adapted microorganisms, but also in bacteria
growing at atmospheric pressure -> life emerged
from a deep sea environment.
Mariana trench - the deepest mud sample
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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.
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
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.
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.
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:
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launch
space vacuum
3 years of radiation exposure
deep-freeze at an average temperature of only 20 K
no nutrient, water or energy source
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
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.
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.
Science 309 (2005)
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
Amber encapsulated bacteria revived
AMG-D1T growing for 48 h at
30oC showing cell division.
International Journal of
Systematic Bacteriology (1998),
48, 511
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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.
Next lecture
Chapter 6. The origin and evolution of life on Earth