Filed under: Uncategorized | Tags: archean, bacteria, cyanobacteria, formation of the earth, hadean, metabolism, oxygen revolution, prokaryote, stromatolites
Here’s a piece of fractal art I created a while ago. It’s my attempt at making a Eukaryotic cell on Apophysis 2.0.
Tell me if you likey or no-likey in the comment box.
Disclaimer: If it wasn’t wholly obvious to everybody reading this blog, none of the media or images reproduced below were created by or belong to me.
NOTE: This post is a little biochemistry heavy (No! Don’t hit that ‘Back’ button just yet!) and it certainly isn’t meant to be taken in in a single sitting. The best way to read this article (and pretty much anything else I write for that matter) would be to skim over the material until you find something interesting. I’ve packed a fair deal of information in here, so I’m sure you’ll find something intriguing amidst the incessant rambling and (I dare say) pedantry. I said I would cover the Cambrian period in this post. I lied.
ANOTHER NOTE: I will repeatedly use the word “Prokaryotic” and “Eukaryotic” in this post. The basic differences between these two kinds of cell-design are summarized below.
Found in Bacteria.
Genetic material consists of a circular ring of DNA that is not bounded in any fashion.
No cell organelles are present.
Characteristic of Plants and Animals
Genetic material (i.e DNA) is contained in a spherical “package” called the nucleus.
Membrane-bound functional cellular components called “organelles” are present within the cell.
As a 1.7 meter tall Metazoan myself, my bias towards large, multicellular organisms is understandable, if scientifically unjustifiable. Since the vast majority of my posts on this blog (hereafter anyway) will deal with animal life and animal diversity, I thought that I might as well devote a single post to the ancient unicellular world of early Precambria – a topic that is rarely dealt with in Television documentaries and other popular media.
To the untrained eye, the biosphere might appear, for the most part, to be divvied up between two great lineages of multicellular life – the Plants and the Animals. Before we proceed to probe through the very deepest and darkest recesses of geological time, we must first dispense with this comfortable fiction. This world of large organisms; of Redwood Pines and Horses, of sea-weeds and tiger sharks and of cacti and desert foxes is, in some sense, just a veneer. Plants and animals occupy a pair of peripheral branches on a tree of life that is not only largely formed by microscopic organisms, but by prokaryotic microbes (namely Archaea and Bacteria) nonetheless.
(The Tree of life – Blue represents bacteria, green represents Archaea and pink represents Plants, Animals and Fungi – get my drift?)
Bacteria are several orders of magnitude more numerous in the soil and in the oceans than even the most populous species of eukaryotic algae and protozoans. They account for a large chunk of the earth’s biomass. However, Bacteria are not important merely because they are abundant – but because they form the basis for several life-sustaining ecological processes (“ecological circuitry” if you will).
If all the plant, fungi and animal species on earth were to disappear tomorrow, many bacterial genera would take a severe beating – especially those that relied on large muticellular organisms for shelter and sustenance. But eventually, the world’s ecosystems would simply revert to the same state they had been in for billions of years prior to the emergence of complex life forms. Cyanobacteria would once again reign supreme in the oceans, stromatolites would rise anew in tidal flats across the globe and many of species of soil bacteria would continue thriving, unfazed by the conspicuous lack of large life-forms.
Now let us imagine the converse of this situation. What if every living species of Eubacteria and Archaebacteria (the two large domains of prokaryotic life) were to disappear tomorrow? Plants and Animals would be starved of nitrogen (critical for the synthesis of proteins). Bacteria are essential for making the free nitrogen in the atmosphere available to plants (and by extension, to us). The sulphur and carbon cycles would also creak to a halt. Carbon would end up trapped in the dead bodies of plants and animals. Ordinarily putrefaction by bacteria converts carbon compounds present in dead organisms into carbon dioxide. This carbon dioxide serves as raw material for photosynthesis (a process that all animals and plants rely on for food). Without bacteria, the amount of carbon being recycled into the air would slowly decrease. It is possible that fungi could take on some of the load (of putrefaction) but they are limited by the fact that they aren’t quite as ubiquitous and rapidly-multiplying as bacteria are.
As Atmospheric Carbon Dioxide concentrations plummeted (because of processes outlined above), the world might also be subjected to a sort of “Global Cooling”, spurred on by the atmosphere’s diminishing stores of greenhouse gases! All said and done, the earth would be a very dead planet within a relatively short span of time.
As such, any attempt at comprehensively studying the history of vertebrate life on earth without first considering the bacteria that, to some degree, made the biosphere itself, is misguided.
The early history of life on earth (a period of time that is rather dismissively referred to as the precambrian eon) is not only a tale of biochemical happenstance and very gradual evolutionary transitions but also of radical planetary-scale changes in atmosphere and ocean chemistry – the likes of which are unparalleled in any succeeding geological period.
NOTE: A discourse on the particulars of abiogenesis (the theory of the origin of life from inanimate matter) might be better suited to a blog on biochemistry. I will therefore ignore the Theory of Abiogenesis, not because it is uninteresting – to the contrary, it involves some of the most sublime questions in all of modern Biology and has attracted such intellectual giants as Dr. Oparin and Dr. Urey – but because I have neither the expertise nor the time to do it justice.
Consider this a very brief introduction to the birth of the earth. The essential ideas contained within the pharagraphs that follow are summarized in small (rather fatuous) snippets printed to the right of each separate title. If you don’t find geology or astrophysics interesting then you should probably skip over this section. As my understanding of these things grows, I will continue to edit this section – so treat it as a work in progress.
1) Clump em’ up! Gas Cloud –> Solid sphere
The planets formed from a swirling mass of gas and dust (principally composed of Hydrogen, Helium and trace a heavier elements) that surrounded the newly forming sun. The Earth formed over 4.5 billion years ago by a gravitationally driven process of compaction and aggregation called accretion. Fragments of matter (hurtling about in the clouds) collided with one another and gradually “coagulated” to form much larger objects (called protoplanets).
2) Molten Planet: Heterogenous Molten Ball –> Beginnings of an inner core and an outer mantle (differentiation)
The energy released by an unending stream of meteorite impacts and the radioactive decay of elements like Uranium (the latter continues to keep the Earth’s interior warm) raised temperatures to a high enough level for iron and many other heavy metals to liquefy. Molten iron migrated to the core of the planet (where it remains to this day) in an event called the Iron Catastrophe. This is why there is very little iron found in the crust of the earth. Notably, this event also gave rise to the Earth’s magnetic field.
The “residual” mantle was largely made up of oxides of iron, silicon and magnesium.
Lighter elements probably accumulated on the surface of this molten planetoid – rather like a film of algae on a pond. Gaseous silicates may have condensed to form the earliest rocks. The primordial atmosphere of the young Earth was initially composed of the two lightest elements – hydrogen and helium. It is likely that raging solar winds from a newly-born sun swept away most of this early “first” atmosphere.
3) A grand collision: Earth + Large protoplanet –> BOOM! –> 10% Larger Earth + Moon
Youtube wont allow me to embed this video, so click here to see what happens when two planets collide.
One popular theory states that, early in its history, the Earth collided with a large planetoid (approximately the size of Mars) called Theia. As a result of this collision, large quantities of material from the mantles of both the impactor and the earth were discharged into outer space. Some of this material would eventually condense to form the moon.
Any remnants of the earth’s hydrogen-helium (and water vapour) atmosphere would have been blown away by the impact. This collision is also probably responsible for the unusual 23 ½ degree tilt at which the earth revolves around the sun (giving us seasonal variations in temperature and climatic patterns).
4) The Early Crust: Oceans of melted rock –> A basalt Crust
In the absence of an insulating atmosphere, the earth cooled relatively quickly. Rocks that vaporized during the collision event condensed within a span of 2000 years. These liquefying rock-vapors left behind an atmosphere of carbon dioxide, hydrogen and water vapor.
Welcome to a world of sulphurous vapors and boiling rocks – a Tartarus beyond the wildest imaginations of Dante or Milton. The earth’s surface was a hellscape of incandescent rock. A burning moon loomed overhead in the skies. Eventually, however, the rock began to cool, and a thin, solid crust was assembled from the magma. This primordial crust was composed, primarily, of Basalt. Evidence has even suggested that this early crust may have undergone processes akin to plate tectonic movement – albeit at a highly accelerated rate.
5) A New Crust: Basalt Crust –> Volcanism + Meteorite Bombardment –> Modern Granite Crust
Despite the formation of a solid crust, volcanism on the early earth continued unabated. Tremendous quantities of magma continued to be belched out by the mantle through breaks in the crust. This early crust was also subject to heavy meteoric bombardment that may have completely annihilated it. Eventually, the basalt (density = 3 g/cm3)proto-crust was replaced by a lighter and somewhat less volatile Granite crust (density = 2.75 g/cm3) by processes that are not yet fully understood.
6) The Atmosphere: Birth of the Atmosphere
Ammonia, hydrogen, methane and water vapor escaped from the crust and slowly accrued to form an ancient atmosphere. This early atmosphere had a pressure 250 times greater than our own (!). There was no oxygen in this atmosphere, and therefore no ozone layer. The land was bathed in deleterious UV radiation making it absolutely inhospitable for living organisms.
7) Neptune Cometh: Birth of the earliest oceans
Seas of liquid water were made possible by the build-up of atmospheric pressure (the chief contributors being the gases mentioned in the previous step). In the absence of any sort of atmospheric pressure, our oceans would vaporize quickly into clouds of water vapor. The Water in our oceans traces its origin to two principal sources:
1) Icy comets and water-rich meteorites may have brought a considerable amount of water to our planet.
2) Leakage from hydrous minerals in the earth’s rocks.
Immense rain-clouds soaked the earth with deluges of water. Water began to fill delevated regions in the earth’s surface and cut waterways through early dry continents.
8 ) The Continents: Landmasses rise up from beneath the waters
Modern continents grew from ancient continental landmasses called “shields” or “cratons”. This process took about 500 million years. These cratons still exist – and are the sources of some of our most ancient rock samples.
The earliest clear traces of life appear in the geological record in sediments laid down during the early Archean, almost 3.5 billion years ago. These organisms are simple photosynthesizing bacteria called cyanobacteria or blue-green algae (they were once wrongly thought to be a kind of algae).
How is it possible for the delicate bodies of microbes to be preserved over the aeons? Indeed, it is a wonder we know anything at all about early history of life! Scientists rely, principally, on three kinds of geological/biogeochemical finds to make sense of early precambrian biology:
1) Chert (also called flint) is a remarkable sort of rock that has the ability to tolerate a great amount of abuse at the hands of Tectonic activity and weathering processes. Small biological features (called microfossils) are sometimes encased within these hardy stones. The rocks themselves are composed of crystalline silica – popularly known as quartz. The lifeforms alluded to the first sentence of this section were preserved in chert from Western Australia (the Warrawoona Group).
2) Stromatolites are laminated accretions of sediments produced by the combined growth, movement and metabolic activity of several kinds of bacteria – and particularly, microbial mats of cyanobacteria. They practically never form in the modern world,with some notable exceptions.
This is a photograph of a Stromatolite I took at the Texas Memorial Museum. Note the layered patterns.
FOOTNOTE: The biological status of the very oldest stromatolites is often disputed. This is because dissolved carbonate and silicate concentrations in the early oceans were high enough for compounds containing said ions to sometimes directly precipitate onto the sea floor and produce structures of non-biological origin that could easily be mistaken for stromatolites.
3) Isotopic signatures. Isotopes are atoms of the same element that differ from one another only by the number of neutrons contained within their nuclei. All organisms that perform photosynthesis take up carbon from the environment (in the form of carbon dioxide) – they just happen to preferentially take up one carbon isotope (C-12) over another (C-13). This preference is slight (and is formally called fractionation), but it leaves a distinct biogeochemical signature in the sedimentary layers. The same principle applies to sulphur isotopes when studying sulphur-metabolizing bacteria.
However, the origins of life must have preceded the cyanobacterial cells mentioned earlier by a fairly large amount of geological time. Cyanobacteria are well-adapted and surprisingly complex organisms, and the world they inhabited was already fully biological. To see the beginnings of organic life, we must track even further back into the Hadean era (over 3.8 billion years ago) – an age of raging volcanoes and cataclysmic meteor showers that preceded the Archean era.
The earliest life-forms were essentially bags of organic compounds like amino acids, simple carbohydrates and lipids (and polymers derived from these basic cellular components) . It would have also contained a replicator molecule like a ribozyme (ribozymes are RNA molecules that are capable of self-replicating, catalyzing metabolic reactions and storing genetic information.). It may have been bound by a membrane composed of phospholipids – these (i.e phospholipids) self-assemble in water to form bilayered membranes and afford some basic selective permeability. Scientists call this Ur-organism, from whence Bacteria, Archea and Eukaryotes come, the Last Universal Common Ancestor or LUCA
Organic compounds are not uncommon in the universe. Colossal interstellar gas clouds containing hydrogen cyanide, formaldehyde and ethanol amongst many other non-biological organic compounds have been detected in outer space.
The earliest living organisms were not bacteria – they were far simpler (Bacteria are, after all, highly evolved and efficient biochemical machines). They were however, as a Russian biochemist by the name of Oparin first suggested, consumers – not producers. They fed on nutrients suspended in the water and derived energy from these foodstuffs without the aid of oxygen.
I often wondered, as a child leafing through my copy of Childcraft’s “The World of Animals” volume, if life could survive on a planet with no oxygen. After a few minutes of contemplation, I surmised (in my infinite ignorance) that it probably couldn’t – not for long, anyway. Imagine my surprise when I later discovered that life on this planet did swimmingly for a billion years with only trace amounts of oxygen (less that 1%) in the atmosphere.
I will try my best to recast the (singularly boring) way metabolism is usually described in text-books. No promises.
As I mentioned earlier (note to self: wow, I write worse than Kant), the earliest organisms were reliant on free nutrients for survival and broke down food substances to release energy in the absence of oxygen. From this we can divine two major themes of metabolic activity.
THE TWO GREAT THEMES OF METABOLOGY
1) The acquisition of Nutrients (Carbon, Hydrogen, Oxygen and Nitrogen or CHON). These nutrients are essential for building lipids, carbohydrates and proteins.
2) The breakdown of said Nutrients to release energy. This requires an energy-release mechanism (like Respiration or fermentation).
All life on earth is predicated on these two processes.
The energy-release mechanism of our early life-form – the simple breakdown of food in the absence of oxygen – is actually called Anaerobic (oxygen-less) Fermentation. The nutrient-acquisition mechanism is termed Heterotrophy (we humans are, in fact, heterotrophs). Heterotrophs are organisms that cannot produce their own food.
As CHON/nutrient supplies began to diminish in the early ocean, new strategies had to be invented.
A little nitrogen please?
Living organisms (now resembling modern bacteria) were faced with their first challenge. Ammonia and Nitrates – which all organisms rely on for nitrogen for the construction of proteins – began to grow scarce. Although atmospheric nitrogen was ubiquitous, even in ancient times, none of it was available for direct consumption.
Some species evolved a piece of costly but critically essential biochemical machinery called the Nif complex. This allows them to assimilate and utilize atmospheric nitrogen for making proteins. This process is crucial, even today, for ensuring the circulation of nitrogen throughout the ecosystem. The Nif complex is found in many species of modern bacteria.
Another challenge quickly became apparent. Like Ammonia and Nitrates, Glucose (a major nutrient from which ancient heterotrophs derived CHO) was fast disappearing from the world’s oceans as it was swept up by the early Archean biology.
Simple Photoautotrophy (photo = “light”, autotrophy =”self-feeding”):
(I will use the terms Sugar, glucose and food pretty much interchangably)
Some life forms began producing their own glucose. They did this by making use of dissolved carbon dioxide (CO2) and light energy from the sun.* They made use of Hydrogen Sulphide (H2S) being pumped out into the oceans through hydrothermal vents as another essential reactant. Free sulphur was released as a byproduct. This process did not release Oxygen. In fact, Oxygen is toxic to these anaerobes. Such bacteria still thrive in the largely oxygen-free abyss of the deep sea. This group of bacteria retained the primitive (and rather inefficient) metabolic process of fermentation* for the purpose of energy release.
C6H12O6 → 2C2H5OH + 2CO2 + energy
sugar ethanol carbon dioxide
* Interestingly, the Sun shone with only 70% of its current light intensity in the Archean. The Moon was also much closer to the earth back then, causing tides several hundred feet high. What a strange world.
A more advanced kind of photoautotrophy evolved amongst a group of organisms that could rightfully be called the first Cyanobacteria. Like their predecessors, they made use of carbon dioxide and light energy to synthesize food – but they used water, not hydrogen sulphide, as a second reactant. Oxygen – the “Molecule that made the World” – was released as a by-product. This is known as photosynthesis. We will have much more to say about this in the next section.
Furthermore, they were capable of aerobic respiration as an energy-release mechanism. Oxygen was not even remotely toxic to these creatures. By using oxygen to burn food substances, Cyanobacteria invented a highly efficient energy-release mechanism – more efficient than bacterial fermentation or even fuel combustion in a modern car.
The Glory of Aerobic Respiration:
As I recounted in the previous paragraph, the Cyanobacteria are capable of breaking down food with the aid of oxygen and thereby releasing energy. Many other bacteria (and our own eukaryotic lineage – the animals) that cannot make their own food, also engage in Aerobic respiration. Aerobic Heterotrophy was the final form of metabolic design to evolve.
This section does not even begin to cover the vast array of metabolic pathways that Bacteria have evolved. Some bacteria respire using nitrates and sulphates. Still others draw energy for the synthesis of glucose not from the sun, but from chemical reactions! Nonetheless, this is a solid introduction for our purposes.
Archea seem to have diverged from Bacteria about 2.7 million years ago. Archea are very distinct from their prokaryotic cousins. For example: they differ, quite significantly, in the structure of their cell walls. Genetic analysis suggests that Archea are more closely related to plants and animals than are Bacteria. They have also evolved an astonishingly large multitude of energy-releasing mechanisms, utillizing methane, hydrogen gas and even metal ions as nutrients.
Archea today are adapted to all sorts of extreme environments – including hot springs, hydrothermal vents, highly acidic lakes and frigid ice-floes. Such levels of tolerance for environmental stress are unheard of elsewhere in the tree of life. This makes them of particular interest to Astrobiologists.
Methane respiring Archea were quite numerous in the Archean ocean prior to the oxygen revolution (recounted below). Today, however, they are outcompeted by more efficient oxygen, nitrate and sulphate respiring bacteria and have been relegated to the bottom sediments of freshwater lakes.
The reduction of methane concentrations (methane being an important greenhouse gas) in the early atmosphere may have helped caused a massive ice age (provocatively called the “Snowball Earth” period). More on this in some later post.
If ever there were a real-life example of terraforming – it happened almost 2.2 billion years ago. It is often assumed that the earth’s atmosphere, save variations in global temperatures, moisture content and precipitation patterns, has been in stasis (with respect to its chemical composition anyway) since the very early history of the earth. This view is patently false. During much of the Hadean and early Archean, Oxygen concentrations in the early atmosphere remained below 1%. This changed, however, with the appearance of Cyanobacteria – a bacterial phylum that has been referred to as “the most important [group of] organisms to have ever evolved” (Knoll).
They rank amongst the most well recorded microorganisms in the fossil record – and for good reason. When subjected to environmental stresses, they often secrete an extracellular sheath of protective filaments. These structures fossilize beautifully. Cyanobacteria also play an important role in building stromatolites (mentioned earlier). Although it is difficult to say with absolute certitude, Cyanobacteria appear to have barely evolved much over the last few billion years – making them the ultimate living fossils!
One of the most far reaching effects of aerobic photoautotrophy was the large scale release of Oxygen into the atmosphere. Some of the consequences of this transition are described below:
1) Oxygen Holocaust: Many anaerobic species of bacteria were annihilated by the toxic (for anaerobes anyway) Oxygen that was quickly spilling into their environments. Photosynthesis may have even evolved as a sort of microbial chemical weapon designed to wipe out competition for resources! Today such anaerobes are relegated to the oxygen-depleted depths of the ocean.
2) Rusting Oceans: 2 billion years ago, Iron concentrations in the ocean were much higher than they are today. Today, Iron is converted almost immediately into Iron oxide (by dissolved oxygen) upon entry into the oceans. In the oxygen-deficient Archean sea, however, Iron was freely circulated throughout the deep waters forming conspicuous geological features called Banded Iron Formations. These Banded Iron Formations disappear some 1.8 billion years into the past.
So why might have free Iron suddenly disappeared from the world’s previously iron-rich oceans?
Oxygen released by cyanobacteria “oxidized” this iron to iron oxide – a process that is commonly known as “rusting”. Hence the title of this post. Slowly, the seas began to loose their greenish cast and take on more familiar hues.
3) The Formation of an Ozone Layer: After the oceans had been largely swept free of ferrous ions (Iron), prodigious quantities of Oxygen began polluting the atmosphere. Oxygen in the upper layers of the troposphere was oxidized to form Ozone. This “ozone layer” shielded the land from the pernicious UV rays of the sun – making the colonization of land by life possible.
This increase in oxygen concentrations could not go on indefinitely (that would have been quite disastrous – small sparks could set whole valleys aflame on a planet with a high enough oxygen level). Oxygen consuming Aerobic respiration performed by Eukaryotes and bacteria eventually stabilized oxygen levels in the air.
We have covered 2 Billion years of Evolutionary History and multicellular life still eludes us. To put this into perspective, the whole extent of Human evolution, from the earliest Australopithecines to modern Homo Sapiens, occurred within a span of approximately 3.5 million years – just0.14% of the time it took to evolve multicellular life. The evolutionary distance between us and the earliest fishes was covered in about one-fifth the time
The world that those tremendous reptilian titans, the Dinosaurs, occupied was much like our own in many respects. It was a world of oxygen, of trees, forests and creatures that could walk, crawl, swim or fly. The Archean earth is not such a world.
Perhaps Mars was once an Archean planet. Perhaps there are thousands of Archean planets scattered across the wide expanse of the Milky Way where life never progressed beyond the unicellular stage. Worlds of silence, empty rockscapes and ocean billows teeming with tiny life.
Margulis, Lynn, and Michael Dolan. Early life: evolution on the Precambrian Earth. Jones & Bartlett Learning, 2002.
Schopf, J. William, and Robert M. Hazen. “Cradle of life: the discovery of earth’s earliest fossils.” Physics Today 52 (1999): 75.
Tewari, Vinod. Stromatolites: Interaction of Microbes with Sediments. Vol. 18. Springer, 2011.
Fenchel, Tom. The origin and early evolution of life. Oxford University Press, 2002.
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