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Early Life and Exolife (split from Exoplanet Stuff)

Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life

In earlier accounts, they were split into Euryarchaeota (methanogens, halophiles, etc.) and Crenarchaeota (mostly hyperthermophiles). They have since been found in numerous environments, and Cren is now a part of TACK or Proteoarcheota.

"In line with their vast diversity, comparative genomics analyses reveal that Archaea are metabolically versatile and are characterized by different lifestyles. Recently discovered archaeal lineages include mesophiles and (hyper-)thermophiles, anaerobes and aerobes, autotrophs and heterotrophs, a large diversity of putative archaeal symbionts, as well as previously unknown acetogens and different groups of methanogens (see the figure)."

"Furthermore, these findings support hypotheses that suggest that all extant archaea evolved from an anaerobic autotrophic ancestor that used the Wood-Ljungdahl pathway and may have been able to obtain energy through methanogenesis."

What Do the DPANN Archaea and the CPR Bacteria Tell Us about the Last Universal Common Ancestors? - Extremophiles as Astrobiological Models - Wiley Online Library

"CPR and DPANN seem to be missing some features thought to be core features of all life. The small genomes, cells sizes and episymbiotic nature of CPR and DPANN may represent an ancestral state."

However, they may represent degeneration from some some self-sufficient state, since these organisms are mostly symbionts.

CPR: in Bacteria, DPANN: in Archaea
 
Phenotypic reconstruction of the last universal common ancestor reveals a complex cell | bioRxiv

Results for the LUCA (all), the LBCA (Bacteria), and the LACA (Archaea):

  • All three had similar-sized genomes: LUCA 2.49 (2.13-2.19), LACA 2.42 (2.05-2.85), LBCA 2.76 (2.25-3.37) Mbp
  • The LUCA and the LACA were ovoid, while the LBCA was rod-shaped
  • All three had dimensions roughly 2 mcm * 0.5 mcm
  • All three had a single cell membrane and a single cell wall
  • All three were motile, with a flagellum
  • All three were salt-tolerant: 0.5 - 50 o/oo
  • All three preferred neutral pH
  • The LUCA and the LACA were hyperthermophiles, while the LBCA was a moderate thermophile.
  • None of the three tended to aggregate (weak inference)
  • All three were free-living and aquatic
  • All three were chemolithotrophs, getting their energy from inorganic substances
That means that all three were autotrophs, like plants, making all their biological molecules from simple raw materials.

Present-day methanogens are much like these three organisms.
 
Charles Darwin - the spontaneous generation of life in some - warm little pond
The letter was mailed to Hooker on February 1st, 1871.

Down, Beckenham, Kent, S.E.
My dear Hooker,

... It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present.

But if (and oh what a big if) we could conceive in some warm little pond with all sorts of ammonia and phosphoric salts, - light, heat, electricity &c. present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter wd be instantly devoured, or absorbed, which would not have been the case before living creatures were formed.
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Which is a big problem with origin-of-life research.
 
Being autotrophs means that the LBCA, the LACA, and the LUCA had a complete set of metabolic pathways for biosynthesis.

Though biosynthesis pathways are often much alike, there are variations in them. A case in point is variations in ribonucleotide reductases (RNA). These take RNA building blocks and turn them into DNA ones by turning their ribose parts into deoxyribise parts, replacing a -OH with a -H. Strictly speaking, the resulting DNA is uracil-DNA or u-DNA, and another step is to take the uracil in DNA building blocks into thymine by adding a methyl group, replacing a -H with a -CH3.

There is not one but three kinds of RNR enzyme, type I uses molecular oxygen (dioxygen: O2), type II is independent of it, and type III is poisoned by it. So something like type II or type III was ancestral, and the author of the first of these papers proposes some ancestral RNR that was different from all three. This ancestral one was then modified into types II and III, and as the atmosphere became oxygenated, type II was modified into type I.

Turning to enzymes that do uracil to thymine in DNA building blocks, they are called dUTPases. I can't find much about their evolution, however.
 
Biosynthesis pathways sometimes have curious variations. For instance, there are two pathways for biosynthesis of the protein-forming amino acid lysine, the diaminopimelic acid (DAP) pathway and the alpha-aminoadipic (AAA) one.

Molecular Evolution of the Lysine Biosynthetic Pathways | SpringerLink - PDF at Molecular Evolution of the Lysine Biosynthetic Pathways - Molecular_Evolution_of_the_Lysine_Biosyn.pdf

The DAP pathway is involved in the biosynthesis of peptidoglycan, a part of (eu)bacterial cell walls. It also has three variants, acetyl, succinyl, and dehydrogenase.

Among eukaryotes, DAP is found in plants and AAA in fungi and euglenids, while both DAP and AAA are found in both prokaryotic domains. They note that DAP is related to arginine biosynthesis, and they propose that it was ancestral. How they think that AAA originated is not very clear.

The primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis | BMC Ecology and Evolution | Full Text

Bacteria have mostly DAP while Archaea mostly AAA.

These authors propose that there was an ancestral pathway common to all three amino acids, and that this pathway split up as a result of gene duplications. AAA emerged first, and later DAP. Both pathways may have present in the LUCA, with its descendants then losing one or the other of them.

The distribution in eukaryotes suggests that the ancestral one had AAA, likely from the archaeal genome host, and that plants got theirs from the cyanobacterium that became a chloroplast.
 
Modern metabolism as a palimpsest of the RNA world | PNAS - 1989 - a classic work, though out-of-date. It's now firmly established that Eukarya is an Archaea-Bacteria chimera, for instance.

But it notes two pathways for biosynthesis of porphyrins:
Two pathways exist for the synthesis of 5-aminolevulinate as the first step in the biosynthesis of tetrapyrroles. One (the Shemin pathway) involves a chemically elegant condensation of succinyl-CoA and glycine dependent on a pyridoxal cofactor. The other (the C5 pathway) involves the reduction of an ester of glutamic acid and RNA, followed by rearrangement of glutamate semialdehyde to give aminolevulinic acid
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Biosynthesis of 5-Aminolevulinic Acid | SpringerLink describes those two pathways and gives their occurrence. Among prokaryotes, the Shemin pathway occurs only in alpha-proteobacteria, and the C5 one in all others.

Among eukaryotes, the Shemin one occurs in animals and fungi, and the C5 one in plants and algae. So one concludes that the ancestral eukaryote carried over the Shemin pathway, and cyanobacteria brought in the C5 one when they became chloroplasts.

So the C5 one was likely in the LUCA and the Shemin one in some ancestral alpha-proteobacterium.
 
Porphyrin contains a ring of rings, the tetrapyrrole ring. But despite that complexity, it's at least possibly prebiotic.
Possible origin for porphin derivatives in prebiotic chemistry--a computational study - PubMed
PREBIOTIC PORPHYRIN GENESIS: PORPHYRINS FROM ELECTRIC DISCHARGE IN METHANE, AMMONIA, AND WATER VAPOR | PNAS

From the palimpsest paper, porphyrins likely go back to the RNA world because their biosynthesis involves RNA, but a similar argument for terpenes is much weaker.

Terpenoid Biosynthesis in Prokaryotes | SpringerLink
A group of metabolites produced by all free-living organisms is terpenoids (also known as isoprenoids). In prokaryotes, terpenoids play an indispensable role in cell-wall and membrane biosynthesis (bactoprenol, hopanoids), electron transport (ubiquinone, menaquinone), or conversion of light into chemical energy (chlorophylls, bacteriochlorophylls, rhodopsins, carotenoids), among other processes. But despite their remarkable structural and functional diversity, they all derive from the same metabolic precursors.
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Terpene Biosynthesis: Modularity Rules - also called isoprenoids

Terpenes are involved in making a variety of biological molecules, like quinones, carotenes, steroids, hopanes, ...

Terpenes have two biosynthesis pathways, mevalonate and MEP. Among prokaryotes, most Bacteria use MEP and most Archaea mevalonate. Most eukaryotes use mevalonates, with photosynthetic ones also having MEP in their chloroplasts (more generally, plastids).


Fatty acids, however, are only in Bacteria and Eukarya and are likely not in the LUCA or its ancestors.
 
On the Origin of Isoprenoid Biosynthesis | Molecular Biology and Evolution | Oxford Academic -- terpenes

Calls the mevalonate pathway MVA.

Looking in Bacteria, the MEP pathway dominates, and the distribution of MVA genes suggests horizontal gene transfer in many case, if not all. Only one of MVA and MEP is present in each species. Examining Archaea, nearly all have the MVA pathway. As to Eukarya, its MVA genes are closest to those in Bacteria, not Archaea, suggesting an odd history, being derived from some bacterium rather than the archaeon that supplied the informational systems.
 
In considering what organisms can survive, our only known example of a biota contains oodles of examples of organisms surviving in conditions that we might think intolerable.
 Extremophile lists:
  • Temperature
    • High
    • Low
  • Concentration
    • Dryness
    • Acidity
    • Alkalinity
    • Salinity
  • Radiation
    • Ionizing radiation
    • Ultraviolet light
  • Pressure
I did a thread on Temperature tolerance of organisms | Internet Infidels Discussion Board and I've found Frontiers | Living at the Extremes: Extremophiles and the Limits of Life in a Planetary Context | Microbiology

 Dissimilatory metal-reducing microorganisms -- they use various metal ions as terminal electron acceptors. Most often iron and manganese, as Fe3+ and Mn4+, reduced to Fe2+ and Mn2+, bot also vanadium, chromium, molybdenum, cobalt, palladium, gold, and mercury.

 List of microorganisms tested in outer space - a sizable number can survive outer-space conditions. Anything that can make a spore, for instance, like some Firmicutes (endospores) and Cyanobacteria (akinetes). Tardigrades are animals that can survive under outer-space conditions, but they do so by drying up, much like those spores.

Bacterial endospores and their significance in stress resistance - PubMed
"Spores are highly resistant to a wide variety of physical stresses such as: wet and dry heat, UV and gamma radiation, oxidizing agents, chemicals, and extremes of both vacuum and ultrahigh hydrostatic pressure."

Survival of akinetes (resting-state cells of cyanobacteria) in low earth orbit and simulated extraterrestrial conditions - PubMed
A proportion of the akinete population was able to survive a period of 10 days in LEO and 28 days in Mars simulated conditions, when the rocks were not subjected to UV radiation. Furthermore, the akinetes were able to survive 28 days of exposure to desiccation and low temperature with high viability remaining. Yet long periods of vacuum and high temperature were lethal to the akinetes.
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Despite this wide range of conditions that organisms can survive in, every Earth organism requires liquid water to metabolize and grow and reproduce. Viruses' extracellular forms, sometimes called virions, are comparable to seeds and spores.

So let us consider when water is liquid. At first sight it seems simple: water melts at 0 C and boils at 100 C. But that's at sea level, and high altitudes lower the boiling point of water. That's why it takes longer to boil an egg in Denver than in some coastal city.

Egg Boiling Calculator - I used US M sized eggs

PlaceAltitude (km)Boil pt (C)Pressure (bar)Soft-egg timeHard-egg time
Sea level01001.01327m 47s10m 51s
Mt. Ben Nevis UK1.34595.580.86188m 29s12m 7s
Denver CO1.64994.560.83028m 40s12m 28s
Mt. Kosciuszko AU2.22892.600.77279m 2s13m 12s
Lukla Nepal2.86090.430.71379m 29s14m 9s
Mt. Whitney CA US4.42184.920.583310m 52s17m 36s
Mt. Blanc Switz4.81083.520.554111m 18s18m 56s
Mt. Kilimanjaro5.89579.520.478712m 47s25m 34s
Mt. Denali AK US6.19478.400.459413m 17s29m 46s
Mt. Aconcagua Arg6.96175.490.412914m 51s-- --
Mt. Everest Np/Tb8.84868.050.314423m 15s-- --
Airliner cruise alt1063.310.2644-- ---- --

I included Lukla because it has the nearest airport to Mt. Everest.
 
Let's now consider  Mars - its surface atmospheric pressure is 6.36 (4.0 - 8.7) millibars or hectopascals. The planet's lowest spot -  Hellas Planitia - has a pressure of 12.4 mbar - and its highest spot - the top of  Olympus Mons - has a pressure of 0.72 mbar.

Vapor Pressure of Water. Calculator | Definition | Formulas -- for Hellas, the boiling point of water is 10.2 C, and for Mars's average surface elevation, close to 0 C, meaning close to the triple point of water, where solid, liquid, and gas coexist: 0.01 C and 6.12 mbar. That means that water is only borderline liquid on Mars.


There is something that can help water stay liquid on Mars: salt. If you have ever wondered why people put salt on snowy or icy roads, it's to lower the freezing point of water so that ice and snow can melt and drain off.

Phase Diagram of Salt Water -  Saline water

At 23.3% by weight of NaCl, table salt, water reaches its lowest liquid temperature: -21.1 C. At concentrations more than that, the salt starts coming out of solution.

For -21.1 C, the vapor pressure of water is 0.9 mbar, extrapolating the pure-water formulas to this low temperature. But salt lowers the vapor pressure of water, and I will estimate how much. Vapor Pressure Lowering states that the vapor pressure is proportional to the mole fraction of water.

For 23.3% by weight, the molar fraction of water is 0.33, and that gives a vapor pressure of 0.3 mbar.

So water can be liquid on Mars if it is salty or in very low places like Hellas Planitia or at some depth below the surface.
 
Let us see what range of temperatures Mars's surface has.  Atmosphere of Mars lists -75 C to 0 C. The top of Olympus Mons is colder by 55 C, and the bottom of Hellas Planitia is warmer by 18 C.

So water can be liquid in Hellas during the daytime.


 Climate of Mars has more temperature values.
Differing in situ values have been reported for the average temperature on Mars,[22] with a common value being −63 °C (210 K; −81 °F).[23][24] Surface temperatures may reach a high of about 20 °C (293 K; 68 °F) at noon, at the equator, and a low of about −153 °C (120 K; −243 °F) at the poles.[25] Actual temperature measurements at the Viking landers' site range from −17.2 °C (256.0 K; 1.0 °F) to −107 °C (166 K; −161 °F). The warmest soil temperature estimated by the Viking Orbiter was 27 °C (300 K; 81 °F).[26] The Spirit rover recorded a maximum daytime air temperature in the shade of 35 °C (308 K; 95 °F), and regularly recorded temperatures well above 0 °C (273 K; 32 °F), except in winter.[27]
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Sources:
 
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That linear lowering of vapor pressure due to solutes is  Raoult's law
Partial pressure p = p(pure) * f(molar)


I now turn from low pressure and temperature to high pressure and temperature. Temperature first. Some organisms can survive temperatures greater than the sea-level boiling point of water.  Strain 121 (Geogemma barossii) got that name from being able to grow and reproduce at 121 C. It can survive temperatures as high as 130 C.  Methanopyrus kandleri does one better: growing and reproducing at 122 C.

M. kandleri has lots of salt and something called cyclic 2,3-diphosphoglycerate; both of them help the organism survive high temperatures. This is further evidence that hyperthermophily is a derived condition.

Not surprisingly, both organisms were found in deep-sea hydrothermal vents, where the water pressure is much higher than near the surface. From Vapor Pressure of Water. Calculator | Definition | Formulas at 122 C, the vapor pressure of water is around 2.15 bar, the pressure for a depth of 11.5 meters. Hydrothermal vents are usually at much greater depths, a few kilometers down, with pressures of a few hundred bar.

For higher temperatures, the boiling-point pressures are: 150 C - 5 bar, 200 C - 16 bar, 250 C - 40 bar, 300 C - 100 bar

The "critical point" of water is at 374 C and 221 bar. At higher temperatures, water continuously fades between its liquid and gas phases.
 
High temperature produces  Denaturation (biochemistry) - loss of non-primary structure - making proteins and nucleic acids unable to function.
Denaturation can also be caused by strongly acidic (low pH), alkaline / basic (high pH), and high-salt conditions.

Denaturation is often done deliberately, as a part of cooking of food. It's usually done with heat, but it's sometimes done chemically, as in  Marination -- adding acids like vinegar or lemon juice -- and in  Brining -- adding water with a high concentration of salt. An alkaline counterpart of marination is used to make  Lutefisk - "lye fish".

Vinegar has a pH of 2 - 3, and lemon juice a pH of 3. Neutral is 7, battery acid 0.9, and lye 13.

Not many organisms can survive high acidity, high alkalinity, high salinity, or high sugar content, so such conditions have long been used as preservatives --  Pickling --  Lutefisk --  Fruit preserves

High salinity and high sugar content work by having too low concentrations of water for many organisms. Water diffuses out of them, and they die of thirst. That is why seawater is dangerous for us to drink -- its salt concentration is about 3 times that in our body fluids -- so we get more thirsty. I like to call this the Ancient Mariner syndrome, after  The Rime of the Ancient Mariner by Samuel Taylor Coleridge (1834)

The Rime of the Ancient Mariner (text of 1834) by… | Poetry Foundation
Water, water, every where,
And all the boards did shrink;
Water, water, every where,
Nor any drop to drink.
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With high enough temperature, primary structure will also go, with the molecules disintegrating. For proteins, "hydrolysis" starts at 150 - 160 C, with water inserting itself between its amino acids:

-NH-OC-
+ H2O ->
-NH2 HOOC-


For pressure, I note that the oceans produce roughly 1 bar of pressure for every 10 meters of depth. Thus, 1 kilometer makes 100 bars.

Let us now consider how water behaves under high pressure: Phase diagram of water and ice and  File:Phase diagram of water.svg at  Ice

Water ice has numerous phases, but most of them are stable only at high pressures and/or low temperatures.

The freezing point of water goes down a degree or so at 100 bar, it is about -7 C at 1 kilobar, and -22 C at a triple point at 2.1 kbar.

The ice goes into phase Ice III, and the next triple point is at -17 C and 3.5 kbar. Then Ice V with the next triple point 0 C 6.3 kbar. Then Ice VI with the next triple point 82 C 22 kbar. Then Ice VII. At 150 C, it reaches 30 kbar, At 225 C it reaches 50 kbar, and at 350 C, it reaches 100 kbar.

This is important for the superdeep oceans that some exoplanets seem to have, because more than a few hundred kilometers down, its water will be frozen as high-pressure ice. That will make it hard for an organism to live there outside of a hydrothermal vent. With an upper limit of 150 C, the pressure thus as an upper limit of 30 kbar, implying a depth of 300 kilometers. To be safer, one may go with a lower temperature, like 80 C, making a pressure of 20 kbar or a depth of 200 km.

So an ocean with depth more than 200 km may be uninhabitable, from inability to get started in a hydrothermal vent.

These depths are for the Earth's surface acceleration of gravity, and they are inversely proportional to that acceleration. So for a smaller planet, the ocean-habitability depth limit will be larger.
 
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