In sexual organisms, species are groups that cannot interbreed under natural conditions, such as humans and horses. Many bacteria and archaea live in different ecological niches that define separate groups, but the ease with which genes can move between microbes makes it more difficult to designate species of microbe. Consequently, genetics is used. A difference of about 2–3 per cent in the genes that code the RNA contained in ribosomes is enough to separate microbial species.
7. The ‘tree of life’ constructed from ribosomal RNA
In fact, we can assess the relatedness of all life forms by comparing genes. For example, genes indicate that you and the fungus between your toes—which are both eukaryotes—are much closer relatives than an archaeon and a bacterium, despite appearances. From the mid 1960s onwards, various techniques have been developed to assess organisms at the molecular level, including a comparison of the sequences of either amino acids in proteins or nucleotides in RNA and DNA.
Genes define the sequence of amino acids in a protein, so differences in the ‘protein sequence’ between species indicate disparity or relatedness. For example, ‘cytochrome c’ is a respiratory protein of 104 amino acids found in many organisms. The sequences are identical in humans and chimps, showing their close relationship. Compared to the human protein, a rhesus monkey has one different amino acid, a dog has thirteen different amino acids, and so on. As species become more distantly related, the protein sequences diverge. With this sort of data, an analyst can draw up a tree, like a family tree, that relates all the species.
In the 1970s, the American microbiologist Carl Woese (1928–2012) used nucleic acids rather than proteins to determine relationships among organisms. He examined RNA in ribosomes (rRNA, for short), with the key insight that this enabled analyses of all life. Protein synthesis, the job of ribosomes, is a core function of any cell. Consequently, the genes that code for rRNA should have mutated slowly over time because most mutations for this process would have been fatal and so failed to accumulate. About 60 per cent of the dry weight of ribosomes is made up of rRNA, and the remainder is protein. Ribosomes in prokaryotes are smaller than in eukaryotes, but otherwise similar in structure and function, allowing their comparison.
Woese isolated a small rRNA and by comparing the differences in the nucleotide sequences, he built a ‘tree of life’ (Fig. 7). The construction of the evolutionary history of organisms in this way is called phylogeny. Woese’s tree was a shock because life grouped into the three domains mentioned earlier, unlike the ‘five kingdom’ paradigm in which archaea were lumped with the bacteria. Furthermore, Woese’s tree demoted plants, animals, and fungi to mere twigs at the end of the eukaryotic branch.
Today, while Woese’s conception of three domains is widely accepted, studies of other genes show that a tree with vertical descent from one generation to the next is too simple. This is because microbes swap genes willy-nilly (Fig. 4), sometimes to unrelated species, which is called lateral (or horizontal) gene transfer. Thus, microbial branches of the tree of life are more like a ‘web of life’, criss-crossed by lateral gene transfers.
Since the mid 1990s, DNA sequencing has become more automated. For sequencing a single gene from environmental samples, the process is as follows: isolate DNA from cells → copy (or ‘amplify’) a DNA gene many times using a procedure called the ‘polymerase chain reaction’ → obtain the gene sequence →compare with other organisms → produce a phylogenetic tree. Increasingly, whole genomes are sequenced, including the human genome, which contains roughly 21,000 protein-coding genes.
Astonishingly, human protein-encoding genes cover only 1.5 per cent of 3 billion nucleotides. The rest of the sequence is said to be ‘non-coding’ or ‘junk DNA’. These terms are actually misnomers because many parts of non-coding DNA regulate when certain genes are expressed (i.e. give rise to proteins) or code for non-protein products such as rRNAs.
The surprising division between archaea and bacteria revealed by genes is confirmed by biochemical differences. For example, bacterial cell walls contain peptidoglycan, which consists of carbohydrate rods cross-linked by proteins, whereas archaeal cell walls have variable chemistry of protein or carbohydrate, or both. Eukaryote cell walls, for comparison, are made of cellulose in plants, chitin in fungi, and are non-existent in animal cells, which have only a membrane. Furthermore, the cell membrane lipids of bacteria and archaea differ. First, there are dissimilar chemical linkages between the hydrophobic and hydrophilic ends of phospholipids. Second, instead of a lipid bilayer with hydrophobic ends dangling face-to-face in the middle of the membrane, archaea have molecules that connect all the way through. This provides strength and is one reason why some archaea can live in very hot water as hyperthermophiles. There are also ecological distinctions. For example, no archaeon is a pathogen, so you’ll never get a disease from archaea whereas you can from various bacteria.
One further use of phylogeny is that the genetic difference between taxa can be related to the time in geological history that they diverged, making a molecular clock. In the 1960s, Emile Zuckerkandl and the Nobel Prize-winning chemist Linus Pauling compared proteins for taxa that were known from fossils to have diverged from a common ancestor. They found that the number of amino acid differences is proportional to elapsed time. One interpretation is that most changes are ‘neutral mutations’ that have no effect on fitness. Similarly, the number of nucleotide substitutions in certain DNA sequences is proportional to elapsed time. Molecular clocks work best with closely related groups of species that are likely to have had similar rates of mutation. Distantly related species have disparate generation times and metabolic rates with variable mutation rates that must be taken into account. To use a molecular clock, a calibration point from the fossil record fixes the date of a particular ancestor in a computer algorithm applied to the molecular data. As we go back very deep into time, there are fewer fossils, so the technique becomes challenging. Nonetheless, molecular clocks indicate that the last common ancestor of animals occurred about 750–800 Ma, which is curious because it predates the oldest animal fossils.
Despite the complications of lateral gene transfers, the tree of life provides information about early life. Thermophiles (microbes that thrive at high temperatures) that grow best at 80–110°C are found near the root of the rRNA tree in the archaea and bacteria (Fig. 7). A reasonable inference is that the last common ancestor lived in a hydrothermal environment. Organisms close to the root are also chemoautotrophs, suggesting that primitive microbes probably gained energy from inorganic compounds. The tree also shows that complex organisms—the plants, fungi, and animals—were late to evolve, consistent with the fossil record. Consequently, if Earth’s phylogeny is a guide for astrobiology, the implication is the same as the fossil record: life elsewhere ought to be mostly microbial for much of the history of the host planet.
Life in extreme environments
Apart from being clustered near the last common ancestor, thermophiles were the starting point for research into extremophiles. Extremophiles are organisms that thrive under environmental conditions that are extreme from a human perspective. In 1965, Thomas Brock, an American microbiologist, discovered pink filaments of bacteria living at temperatures of 82–88°C in a steamy hot spring in Yellowstone National Park. At that time, no life was known to exist above 73°C, so Brock’s discovery spurred an interest in exploring the limits of life.
Although it wasn’t anticipated, Brock’s efforts also ultimately enabled the explosion in genetics. Brock found a new bacterium, Thermus aquaticus, in another hot spring. From this microbe, industrial scientists isolated an enzyme stable at high temperatures that was able to catalyse the polymerase chain reaction (PCR)—the DNA duplication technique that revolutionized biology. Thus, pure science—in this case, what we now call astrobiology—ended up benefiting society unexpectedly. Today, PCR technology is a multibillion-dollar industry. Brock, however, gave away his bacterium and didn’t get a penny.
Often, the grow
th (meaning replication) of extremophiles either requires extreme conditions or is optimal at them. For temperature, the upper limit for eukaryotes is 62°C, compared to 95°C for bacteria and 122°C for archaea. The record holder, the methane-producing archaeon, or methanogen, Methanopyrus kandleri, has optimal growth at 98°C.
Identification of various extremophiles (Box 1) indicates that life exists in a much wider range of environments than anyone thought feasible fifty years ago, which opens up possibilities for life beyond Earth. For example, thermophiles might survive deep underground on Mars because they exist deep in the Earth’s crust. Another example concerns life in Lake Vostok (250 km long, 50 km wide, and 1.2 km deep), which sits below 4 kilometres of ice in east Antarctica. Ice some 100 metres above the lake is thought to have frozen from lake water. Oddly, it contains traces of the DNA of chemoautotrophic thermophiles. This suggests that beneath the cold lake (at –2°C because of the high pressure), there may be hydrothermal water containing thermophiles emanating from fractures. The techniques honed for detecting life in lakes such as Vostok can be applied in the search for life elsewhere in the Solar System. Sampling for life in the subsurface ocean of Jupiter’s moon, Europa, involves similar challenges.
Box 1 Extremophiles
Acidophiles: require an acidic medium at pH 3 or below for growth; some tolerate a pH of below 0.
Alkaliphiles: require an alkaline medium above pH 9 for optimal growth and some live up to pH 12.
Barophiles (or piezophiles): live optimally at high pressure; some live at over 1,000 times the Earth’s atmospheric pressure.
Endoliths: live inside the pore space of a rock (endo = within, lithos = stone).
Halophiles: require a salty medium, at least a third as salty as seawater (halo = salt).
Hypoliths: live under stones (hypo = under).
Psychrophiles: grow best below 15°C, while some grow down to –15°C, with reports as low as –35°C for metabolism.
Radioresistant microbes: resist ionizing radiation, such as from radioactive materials.
Thermophiles: thrive at temperatures between 60 and 80°C, while a hyperthemophile has optimal growth above 80°C; they can be contrasted with mesophiles, such as humans, which live between 15 and 50°C.
Xerophiles: grow with very little available water, and may be halophiles or endoliths (xeros = dry).
Chapter 6
Life in the Solar System
Which worlds might be habitable today?
In 2002, while teaching astrobiology, I offered a prize to any student who could guess nine celestial bodies up to the orbit of Pluto that I reckoned might possibly harbour extraterrestrial life (Table 1). No one won. But, with the growth of astrobiology discoveries and online information, someone received the prize in 2010. Today I might add several more bodies, but we’ll leave those until the end of this Chapter.
The type of life that I’m considering in Table 1 is simple, comparable to microbes, and the guiding principle concerns liquid water. On Earth, wherever we find liquid water, we find life, whether in bubbling hot springs, drops of brine inside ice, or films of water around minerals deep in the crust.
Some go further and speculate that weird life—organisms that don’t depend on water—might exist in lakes on Titan, the largest moon of Saturn. Titan’s lakes contain liquid hydrocarbons, not water, somewhat like small seas of petroleum. Life that uses hydrocarbon solvent is unknown, and there are some arguments from physical chemistry, which I’ll mention later, that such life might be difficult. In contrast, there’s no question that liquid water can support life.
Table 1. Nine abodes where life might exist in the Solar System today. The distance to the Sun is in Astronomical Units (AU), where 1 AU is the Earth–Sun distance of about 150 million kilometres or 93 million miles
Body
Type of body and average distance from the Sun
Why it might have life
Mars
planet, 1.5 AU
might have subsurface pockets of liquid water
Ceres
largest asteroid, 2.8 AU
might have a subsurface ocean
Europa, Ganymede, Callisto
large icy moons of Jupiter, 5.2 AU
evidence for subsurface oceans
Enceladus
icy moon of Saturn, 9.8 AU
evidence for a subsurface ocean or sea and presence of organics
Titan
largest moon of Saturn, 9.8 AU
evidence for a subsurface ocean and presence of organics
Triton
largest moon of Neptune, 30.1 AU
might have a subsurface ocean
Pluto
large Kuiper Belt object, 39.3 AU
might have a subsurface ocean
Sunlight and the habitability of the inner planets
Whether the inner planets—Mercury, Venus, Earth, or Mars—have liquid water mostly has to do with temperature and, thus, distance from the Sun (Table 2). ‘Location, location, location’ doesn’t just sell houses but is critical for planetary habitability.
Table 2. The inner planets and factors that affect their current habitability
Location matters because sunlight spreads into a sphere with a surface area that grows with the square of the planet–Sun distance. Solar flux is the wattage (like a light bulb) of sunlight received per square metre. At the Earth’s orbital distance of 1 Astronomical Unit (AU), sunshine provides 1,366 Watts over every square metre, the equivalent of almost fourteen 100-Watt light bulbs. At the 5 AU distance of Jupiter, the solar flux is a factor of 25 times smaller because the same energy spreads over a sphere that has 5 × 5 = 25 times the area. For Mars, at 1.5 AU, the solar flux is 2.25 (= 1.5 × 1.5) times smaller than for Earth. In contrast, Venus, at 0.72 AU, receives solar flux almost twice as big as that of the Earth.
Mercury, at only 0.4 AU from the Sun, is lifeless. It’s the smallest of the eight planets (about two-fifths the diameter of Earth) and has no liquid water and probably never did. Today, Mercury’s barren surface sometimes reaches 430°C. If Mercury once had an atmosphere, it would have burned off when Mercury formed because of low gravity and intense sunlight.
The distance from the Sun explains why Venus and Mars are hostile to life, although that’s not the whole story. The roughly 460°C surface of Venus is even hotter than Mercury gets, while Mars is an icy desert with an average temperature of –56°C. Venus is comparable in size to the Earth, but Mars is smaller—around half the diameter and one-ninth the mass of Earth. In fact, Mars’s small size led to its poor habitability today, as we’ll see later.
Although solar flux is one factor, the greenhouse effect on Mars and Venus also determines surface temperatures. The Martian atmosphere exerts only 0.006 bar surface pressure, compared to Earth’s 1 bar. This wispy air is an arid mix of 95.3 per cent carbon dioxide, 2.7 per cent nitrogen, and minor gases. Recall that Earth’s greenhouse effect is 33°C. Because of atmospheric thinness and dryness, Mars’s greenhouse effect is only 7°C, which leaves the planet frozen. The two main gases in Venus’s atmosphere, 96.5 per cent carbon dioxide and 3.5 per cent nitrogen, have similar proportions to those on Mars. But in stark contrast, Venus’s atmosphere is massively thick and has a huge pressure of 93 bar at an average ground elevation. As a result, Venus’s greenhouse effect is a whopping 507°C, i.e. 500°C bigger than on Mars (Table 2). The upshot is that neither planet’s surface supports liquid water. In the thin air on Mars, a puddle would boil (or rapidly evaporate) and freeze at the same time, and water generally exists only as ice or vapour. Meanwhile on the scorching surface of Venus, liquid water is impossible.
Without liquid water, Venus is considered by most astrobiologists to be lifeless. A few speculate that acidophile microbes might live in its clouds of sulphuric acid particles. However, I doubt it. Apart from the lack of available water, atmospheric turbulence would pull microbes down into Venus’s inferno or up to fatally desiccating heights.
Was Venus inhabited
in the past?
Venus is still astrobiologically interesting because it may once have had oceans and life. It should have begun with plenty of water because the amounts of other volatiles are similar to Earth’s. (Volatiles are substances that can become gases at prevailing planetary temperatures.) For example, if you took all of the Earth’s carbonate rocks and turned them into carbon dioxide (CO2), the Earth would have about ninety atmospheres’ worth of CO2, like Venus. If you extracted all the nitrogen in minerals on the Earth and added it to the Earth’s atmosphere, you would get almost three atmospheres’ worth of nitrogen gas, which again is similar to that in Venus’s atmosphere. Because accretion of hydrated asteroids was the ultimate source of carbon and nitrogen on Venus and Earth, it’s reasonable to infer that Venus also gained lots of water from them, as the Earth did.
Unfortunately Venus was doomed by its proximity to the Sun because of a runaway greenhouse effect. When baked by intense sunlight, the evaporation of water can make an atmosphere so moist that it becomes completely opaque to the infrared radiation emitted from the planet’s surface. At this point, there’s a limit to the cooling of the planet by emission of infrared radiation to space, which is set by the properties of water and a planet’s gravity. Recent calculations suggest that this runaway limit is about 282 Watts per square metre for Earth and a few Watts less for Venus.
To understand the runaway limit, consider turning Earth into Venus. As mentioned earlier, the solar flux at the Earth’s orbit is 1,366 Watts per square metre but the Earth reflects 30 per cent of this and so absorbs only 70 per cent. Then an additional reduction of 50 per cent comes from having only half of the Earth in daylight, and a further 50 per cent decrease accounts for glancing sunbeams on Earth’s curved surface. Putting all these factors together, the Earth absorbs a net (0.7 × 0.5 × 0.5) × 1,366 = 240 Watts per square metre of sunlight. When stable, the Earth emits the same amount of energy into space in the infrared and so keeps a constant global average temperature. But imagine if the Earth were moved to the orbit of Venus, where the absorbed sunlight per square metre would double from 240 to 480 Watts. The ocean would become like a hot bath and the steamy atmosphere would reach the runaway limit where only 282 Watts per square metre can radiate into space. With more energy per square metre coming in (480 Watts) than going out (282 Watts), the Earth would simply get hotter and hotter. The entire ocean would evaporate and surface rocks would melt. At that point, near-infrared light from a searing upper atmosphere would shine through to space, so that the incoming sunlight and outgoing radiation would come back into balance and the surface temperature would plateau around 1,200°C. This nasty process is what we think happened to Venus. Any Venusians would have been toast.
Astrobiology_A Very Short Introduction Page 9
