3.1.1 The bacteria
220.127.116.11 The common ancestor
Debate on the origin of life centers on the question as to whether the cradle of life is hot or cold. With no fossils to rely on, indirect clues are evaluated. The hotter the environment, the more difficult will life have to assert itself because the polymers on which life relies (proteins and nucleic acids) are heat-sensitive. Yet, the primeval earth was presumably hot and thermophilic bacteria do exist. Either these bacteria are the ancestors from which all subsequent life derives, as suggested by Woese in 1987, or else they are secondary adaptations of life that would have originated from a mesophilic bacterium, thriving in temperate surroundings. Recent analysis of the G-C ratio of ribosomal RNA from diverse organisms 1 points to a mesophilic ancestor while geological considerations point to a thermophilic ancestor.
There exist bacteria that live at about 250°C. The bottom of the oceans is dotted with volcanoes, geysers and springs where water and magma extrude. Today, the upper layers of oceans are rich in oxygen, produced by the phytoplankton. Intermediate layers are deprived of oxygen. The ocean bottom waters are hyper saturated in oxygen. The origin of this bottom layer oxygen is presumably due to underwater volcanic activity. The hydrothermal sources, discovered in 1977, produce local temperatures as high as 350° C under ocean water pressures of 250 to 260 bars. The hydrothermal fluids provide an abundance of nitrates, sulfates, CO2, and sometimes molecular oxygen, which are used by autotrophic bacteria (Thiobacillus and Thiomicrospira). These chemosynthetic bacteria apply these mineral sources of energy to the synthesis of ATP necessary to transform mineral carbon (CO2) into organic carbon. These bacteria are remarkably well adapted to growth under those extreme conditions of pressure and temperature. At 250 °C and under 265 bars, they need only 40 minutes to divide. Their density in hot sources is as high as 109 cells per milliliter, which corresponds to 1 gram of bacterial living matter per liter. For bacteria, such a cellular density is very high2.
Today, the vents supply nutrient-loaded hot water supporting oases of tubeworms, mussels, and crabs in the vast desert of the ocean bottom. However, hydrothermal sources are transient. Their activity lasts no longer than about 30 years, after which they terminate, to resume somewhere else. The local temperature then drops at once from a high of 350°C to a low of 2°C, which is the mean water temperature at the ocean bottom. These dramatic and sudden variations -which need not have been so pronounced during primeval times-, are a violent evolutionary pressure towards adaptive measures, such as resistance to a drop in oxygen pressure.
One may hypothesize that these bacteria are the last representatives of the paleobacteria that populated the earth in early times. The resistance they show to hot surroundings is due to at least two adaptations. First, their double-stranded genetic material consists mainly of G-C pairs, which are more resistant to heat than A-T pairs of nucleotides. Second, basic proteins stabilize the nucleic acid double-strand. Also, the proteins composing the ribosomes of heat-resistant bacteria are in general more basic than are those of heat-sensitive ones. This increased basicity would favor the stabilization of nucleic acids needed in the warm to hot environment prevalent during the early ages.
More evolved bacteria would then be the eubacteria, whose group includes the bacteria able to withstand oxygen pressure, and also the blue-green algae, and the next evolutive level would be the eukaryotes. As said supra, another possibility is that the thermophilic bacteria are a secondary adaptation to hot environments.
Bacteria are endowed with a system of assimilation of nutrients that is much more versatile than the systems exhibited by less evolved forms of life. Chemical substances are directly, and with some degree of efficiency, transformed into the fundamental building blocks of living matter. These building blocks, i.e. nucleotides, amino acids, sugars, etc. are kept to high concentrations within the bacterial cell and thereafter assimilated according to a refined process: a single-stranded nucleic acid called messenger RNA is synthesized on a portion of the bacterial double-stranded DNA gene. This messenger RNA is an exact copy, with a minor change in the composition of the sugar and another in one of the bases, of one of the two DNA strands. The messenger RNA released by the DNA passes through a series of aggregates called the ribosomes. The genetic information carried by the messenger RNA is translated into protein during its passage through the ribosomes
Figure 3.1. The protein- synthesizing mechanism in use in bacteria and eukaryotic cells consists of a repository of the genetic material composed of double-stranded DNA. A Messenger RNA is synthesized on this DNA. The message carried by the messenger RNA passes through ribosomes where it is translated into proteins with the help of a transfer RNA that mediates this translation. This is thus the way enzymes and other proteins are synthesized. The system has been kept for the purpose of protein synthesis in eukaryotes, including man, with various details changed.
Some bacterial proteins are synthesized without the help of ribosomes. Giant enzymes synthesize these short proteins. They are mostly peptides (e.g. penicillin and cyclosporin) used for critical tasks such as killing parasites and communicating with members of their own species.
This bacterial system of assimilation of chemical substances is controlled by feedback mechanisms. An excess of final products synthesized in great enough quantities will command the halt of their own production. On the other hand, the appearance of a new source of energy in the environment will trigger the synthesis of the enzymes necessary to assimilate it. The life of bacteria is thus modulated. This modulation is in part done by a simple derivative of nucleotide, cyclic adenosine monophosphate (cyclic AMP) (fig.3.2).
Figure 3.2. Chemical structure of cyclic AMP.
This cyclic AMP is a primitive messenger that hooks onto particular stretches of the bacterial DNA. By doing so, it allows some part of the genome to be copied into a messenger RNA and translated into protein. This cyclic phosphate does not necessarily regulate all genes of bacteria.
18.104.22.168 Bacterial multiplication
When bacteria are grown as a suspension in a liquid medium, under optimal conditions, they multiply very fast and the container appears full within 3 days of culture. However, even if numbers are phenomenally high, the total mass of living matter present is very small, when compared with the mass yielded by eukaryotic cells grown in culture, such as yeasts and of course with the density of the living matter of our own bodies.
The division in two of the bacterium itself occurs when an enzyme engineers the duplication of the DNA. Once a new DNA double strand is made, the cell is in possession of two sets of genes. It thereafter simply splits into two daughter cells, each carrying one genome. This system of cell division has been retained with adaptive variations throughout further evolutive levels. It currently takes place in our bodies during the regeneration of liver, skin, blood, nails and other components. In eukaryotes, a double-set of genes occupy the two daughter cells, which is not the case with bacteria.
At the lowest organizational levels of the animal kingdom and also plants, this ability of cell generation allows an organism that has been cut into several pieces to rebuild whole entities again (worms, planarians, jellyfishes, sponges). This ability of cell regeneration, leading to the rebuilding of whole organs and whole organisms, is lost in more evolved species, including Man, for specialized cells as those of the heart, muscle, brain, eye. In these particular cases, damaged cells are usually not replaced.
The duplication of the genetic material, the formation of messenger RNA’s and the mechanism of protein synthesis in prokaryotes are adjuvanted by several enzymes. This job of transforming raw genetic information into proteins appears critical and was, from the beginning of the discovery of the system, supposed to be precise and fast. There is a growing body of evidence3 that the system is highly inefficient and operates in chaos. The transcription machinery is orchestrated by the RNA polymerase I, which consists of at least a dozen different proteins that need to assemble on a gene to engineer the synthesis of RNA from DNA. The polymerase does not smoothly assemble on a gene, as was supposed for a long time, but each of the proteins collides without sticking, and a polymerase protein would wait for only 2 seconds for another to show up and bind to it. It leaves if their companions are seconds behind schedule. Not only is the assembly of the polymerase I hazardous, but a formed polymerase breaks apart once it has transcribed a gene, forcing reassembly to start from scratch. The scientists who seek purpose in cellular machinery may not find it: the driving force may very well be only random chance events. Despite this stunning inefficiency, the abundance of the polymerase proteins is such that a polymerase assembles every 1.5 seconds.
Fast protein synthesis provides such living systems with a tremendous selection advantage not substantially impaired by the small disadvantage of the need to pair complementary bases. Whereas a chemical duplication of RNA proceeded with a chance of error in replication lying at about 1 for 100 bases copied, the presence of a refined replication mechanism in bacteria reduces this hazard considerably, to 1 in 1,000,000 bases copied.
If one assumes that the incorporation of one single faulty base within the genetic system of an organism results in its death, then the precision of the duplication mechanism acquired by bacteria will allow the increase in genetic material to about one million bases without the appearance of lethal changes. All mutations of bases are however not lethal, so that the number of bases may be higher than a million, 3 to 6 million, which is in fact the number of bases usually found in the DNA of bacteria. Assuming that one gene of standard size produces one messenger RNA, that in turn commands the synthesis of one protein, this number of bases is sufficient to command the formation of about 1,000 proteins of standard size. With a much higher value for the number of bases, an error-free reproduction only rarely takes place. A bacterial species endowed with a too large amount of nucleic acid would soon disappear on account of lethal errors in DNA replication. However, if the size of the genetic material is kept around the value of 3 to 6 million bases, considering that replication errors in the DNA will sometimes be harmless or even useful, a divergent phase of evolution will start, in which many bacterial species have comparable chances of survival (fig 3.3).
The search for fossils in rocks formed before the Cambrian explosion of life 540 million years ago has been plagued by misinterpretations and questionable results. Microscopic squiggles in a 3.465 billion-year-old Australian chert were claimed in 1993 to be fossilized bacteria. Chert is a very hard quartz, i.e. hydrated silica, containing impurities. These bacteria, of whom some were thought to be oxygenic blue-green algae (cyanobacteria for the scholar), were thus the oldest, coming just 400 million years after the last lethal bombardment of the young planet. This is now disputed and these squiggles were argued in year 2002 to be lifeless minerals produced by a hot-spring conduit that eventually clogged with chert.
Live bacterial cells inhabit sediments as far as 1 kilometer beneath the sea surface. These communities may account for as much as one-third of Earth’s biomass. Primitive unicellular organisms having the appearance of bacteria have been found in rocks originating from deposits accumulated by sedimentation in water in South Africa. These rocks are about 3 billion years old. Since the earth was formed about 4.5 billion years ago, it took at the most 1.5 billion years to devise an autonomous mechanism of life that engineered an immense transformation of the environment.
The mechanism is mainly based on the exploitation of the available glucose. The destruction of 180 grams of glucose by bacteria produces heat, 88 grams of CO2 gas and 92 grams of ethyl alcohol. The energy so released is stored by bacteria in newly synthesized adenosine triphosphate (ATP). This ATP will in turn continue the process of glucose degradation. The effectiveness of this operation is, however, low: the net gain in ATP of this operation amounts to only a 3% yield. The process was, however, the only one available for many thousands of years and was instrumental in releasing large amounts of heat, alcohol and CO2 gas into the atmosphere. We noted earlier the possibility that methanogenic bacteria were preponderant in early times and brought the temperature of the earth to within a few degrees of its current temperature.
Mineral sources of energy were also exploited and six species of bacteria are known to reconvert sulfur into a form suitable for higher organisms The sixth species was discovered in 1999. This giant sulfur bacterium, visible to the naked eye was found along the coast of Namibia (H.N. Schultz et al. Science, 284, 493-495, 1999). Histones and protamines, which are at the core of the reproductive system of eukaryotes, are devoid of sulfur, indicating that eukaryotic cells may have developed before suitable forms of sulfur became available. Most superior organisms, including Man, have proteins that contain sulfur. This sulfur stabilizes proteins in a very significant way and does so only in the presence of oxygen, indicating that they developed after sizable amounts of free oxygen were available. The absence of sulfur-reconverting bacterial species would have meant that superior living forms either would have done without sulfur or else that they would have developed a mechanism of production of suitable forms of sulfur. Another imaginable possibility is the existence of no superior life at all.
An absolutely essential service rendered by bacteria to all life on earth is the fixation of atmospheric nitrogen, i.e. the transformation of nitrogen into a form suitable for use by all superior life, which absolutely needs the nitrogen atom to thrive and multiply. Nitrogen is present in the air under the form of nitrogen gas (N2) at the high concentration of 79%. Under this form, higher organisms cannot assimilate it. Presumably, nitrogen was initially present under the form of ammonia (NH3) and it was this ammonia that bacteria used. With the disappearance of ammonia they must have switched to N2; they are now the only ones able to fix atmospheric nitrogen and reconvert it into a form suitable for higher living forms.
Another vital function fulfilled by bacteria arose after the production of molecular oxygen. Ozone (O3) is the only shield that now exists on earth against lethal UV radiations. This ozone is formed in the high atmosphere under the influence of light at wavelengths below 242 millimicrons. Yet, ozone is by no means adequate to support life and there should not be too much of it. Ozone is destroyed either by UV light or by direct interaction with an oxygen atom. However, the rate of destruction by these mechanisms is twice as slow as the rate of production, so that the ozone produced from the large supplies of oxygen now available would very rapidly oxidize all living matter. The dynamic balance between a production and destruction adequate for Life to continue on this earth in its present form is provided by another destruction mechanism devised by bacteria.
Considering the formidable biomass that represent bacteria within the lithosphere, one should not ignore geospheric evolution, which covers hundreds of millions of years4. The earliest deposits of sedimentary iron, hematite (α-Fe2O3) and magnetite (Fe3O4), with a total thickness of several hundred meters, appear about 3.6 billion years ago. Red ferric iron oxides formed less than two billion years ago in the presence of oxygen. More recently formed iron deposits are not known, which indicates a unidirectional evolution of the geosphere. Where did the iron and the oxygen come from?
Primitive blue green algae appeared 3.5 billion years. Iron bacteria and true blue algae (cyanobacteria) were present 2 billion years ago. Ordinary iron bacteria produce ferrihydrite (Fe (OH)3. nH2O) that rapidly transforms abiogenically into hematite (α-Fe2O3). The biogenic reduction of ferryhydrite into magnetite (Fe3O4) is achieved by thermophylic proteobacteria such as Geobacter metallireducens that reduce the iron oxide. Hydrogen at the low concentration of 1 part per million is sufficient for the process to efficiently proceed.
The second product of bacterial geospheric activity concerns sulfur: the formation of sulfates is a biogenic process produced through the oxidation of sulfides by sulfur bacteria. The final product is pyrite (FeS2): some Precambrian micro-fossils are full of pyrite crystals. With the help of oxygen, other bacteria, as thiobacillus, transform the pyrite into sulfates that dissolved in the oceans, whereas the iron is ultimately transformed into metal oxides, as hematite. One sees, thus, that the sulfur and iron cycles of the proteobacteria served as sinks for excessive photosynthetic oxygen produced by blue green algae. Communities of bacteria and cyanobacteria thriving 2 billion years ago were probably the movers of the oxygen revolution. These communities are today a rarity and exist in hyper saline marine lagoons. In early days, they had no competitors and were probably ubiquitous.
22.214.171.124 The bacterial evolutive dead-end
Most of the DNA present in bacteria is used for the synthesis of proteins; not much of it lies idle. This DNA is made of between 3 and 6 million bases allowing the production of about 1,000 proteins. The presence of larger amounts of usable DNA that would permit the production of more proteins can be envisioned only if the errors in replication of the bacterial DNA drop below the level of one false base for one million replicated.
Such a reduction in the frequency of error is found among certain bacterial species. For example a common parasite of the human intestinal tract, Escherichia coli, has a probability of error in DNA replication as low as 10-8. This hundred-fold reduction over other bacterial species is presumably the result of the acquisition by Escherichia coli of a mechanism of pseudo-sexuality. Sometimes a bacterium within a dense population approaches another bacterium and inoculates in this "female" its own genetic material, a string of DNA. A still simpler phenomenon of gene pooling is the release of small pieces of genetic material within the surrounding environment. Certain bacteria within a colony pick up these free wandering pieces of genetic material and include them within their own genes.
These two systems of genetic exchange, conjugation and transformation (fig. 3.4), have been conserved in more developed cells and currently take place in cultured colonies of cells of human origin. That it also takes place in our bodies is plausible but not yet certain. This phenomenon of gene pooling occurs also in plants and is the reason why genetically modified plants (e.g. corn) are ostracized in some European countries, by fear that the modified genes would be taken up by other organisms.
Figure 3.4. Conjugation is a mechanism of gene pooling wherewith the genetic material of one bacterium passes to another recipient bacterium. Cell contact is required for this transfer. Transformation consists in the release of small pieces of DNA into the environment. Receptive cells will pick up these pieces.
An exchange of genetic material by lateral gene transfer can thus occur between two bacteria. The "female" individual receives advantageous material and undergoes a series of cell divisions that allow, by a simple phenomenon of selection, the displacement of all the less favored strains. As a corollary to this genetic exchange, a mechanism of exclusion had to be devised also. Indeed, if organisms that acquired a favorable trait were able to pass it indiscriminately along to any other organism that happens to be around, this favorable trait has many chances to be lost, because not all other organisms can usefully integrate it. The appearance of a system of genetic exchange must have been coupled with a system of restriction that would have kept the exchange to individuals able to usefully exploit it. And this is a simple explanation for the appearance of species.
The contemporary strenuous search for the common ancestor relies heavily on ribosomal RNA phylogeny. However, lateral gene transfer is not uncommon among different bacterial species and bacterial genomes contain genes from multiple sources. As a consequence, the history of primitive life cannot properly be represented as a tree. A reticulated tree or net might more appropriately represent life’s history (Phylogenetic classification and the universal tree. W. Ford Doolittle, Science, 284, 1999, pages 2124-2128). In primeval times, species of bacteria were probably not as stringently defined as today and lateral gene transfer must have been common and widespread. Horizontal gene transfer is the product of highly selective evolutionary events that are not a minor element of either prokaryotic or eukaryotic evolution. The significance of lateral gene transfer for bacterial evolution was recognized when drug resistance emerged on a worldwide scale. The facility with which certain bacteria developed resistance to antibiotics indicated that this trait was not generated de novo by each species but was transferred among species. Lawrence and Ochman5 showed that, in the 100 million years following the divergence of Escherischia coli, a common bacterium that multiplies in our guts, from Salmonella, a mammalian pathogen, 755 genes have been introduced from many sources into the Escherischia coli chromosome by more than 230 lateral transfers. Between 10% and 16% of the chromosome of Escherischia coli arose through lateral gene transfer, often from very divergent organisms, as eukaryotes or Archaea. Sixteen thousand bases per million years have been introduced successfully into the E. coli genome.
Antibiotic resistance allows a microorganism to expand in the presence of noxious compounds and antibiotic resistance genes are highly mobile genetic elements. Virulence genes are also genes easily acquired by lateral transfer. Likewise, lateral gene transfer of metabolic properties (e.g. the capacity to metabolize lactose instead of or in addition to glucose) has played a significant role in bacterial evolution because recipient organisms are therewith allowed to explore new environments. From this, it is clear that most ecological innovation in bacteria is fundamentally different from the diversification in multicellular eukaryotes.
If the advantages of the pseudo-sexual conjugation are to be maintained during the subsequent selection process, the favored bacterial strain must endeavor to be well protected from errors in DNA replication, lest it will lose forthwith the advantages gained during conjugation. If the probability of error is maintained at 10-6, the favored strain will be able to assert itself only with extreme difficulty over its competitors. The 100 fold lowering of the probability of error in replication observed in E. coli over other bacteria is thus an imperatively needed character. It was presumably acquired and developed through evolution in multiple steps.
These evolved bacterial species have developed mechanisms for the repair of damage inflicted to elements of information by thermal blows or nuclear radiations. These were presumably both of a higher level earlier in time than they are today. The proteins directing the synthesis of new DNA in these evolved prokaryotes are capable of suppressing in a significant way the occurrence of spontaneous mutations. Also, they are able to avoid the consequences of lesions received, by reinterpreting the different mispairing bases included in the DNA chain. In these prokaryotes, the enzymes associated with the replication of the genetic material play a crucial role in the selection of the correct base during DNA replication. This character granted immediate survival advantages to the selected bacterial system over more primitive organisms devoid of it.
The reliance of bacteria on synthesizing enzymes for the reduction of errors in replication did not allow a reduction beyond the level of 10-8. Accumulation of larger amounts of information into the genetic material was thus ruled out. Another attempt towards higher complexity in bacteria is a tremendous increase in length (fig.3.5) or else an aggregation of several single units into colonies. However bacteria possess a cellular membrane that is extremely tough. It is not well suited to enter in communication with other units. The maintenance of a tough membrane is a hindrance to cellular communication.
Figure 3.5. Proteus vulgaris is a big ciliated bacterium very common in soil and sewage. It is frequent in end-to-end pairs and short chains. Other bacteria as Streptococcus present the same feature.
The bacteria multiplied profusely, thriving on available nutrients such as glucose. Yet, the supply of nutrients available could not but dwindle in the course of time and bacteria were fully dependent on it. It was not in their power to escape from this dependency because they could not synthesize nutrients of the type needed for their survival. Bacterial evolutive divergence conducted the whole group to a dead-end.
Excluding the blue-green algae, which are the only oxygenic bacteria, five groups of photosynthetic bacteria exist. On the basis of phylogenetic analyses and the complexity of the photosynthetic machinery, these simple anoxygenic organisms almost certainly preceded the cyanobacteria (blue-green algae). Four of them 6 use light as a source of energy to assimilate CO2 and make ATP, with the help of a bacteriochlorophyll and carotenoids but however without the help of oxygen. They are unable to use water as a hydrogen donor to reduce CO2 to organic matter with the production of O2 as a metabolite and they rely on hydrogen, ferrous iron and reduced sulfur compounds as reductants. They also have oxygen-independent respiration. These anaerobic anoxygenic phototrophs are not very successful. A fifth group, aerobic, is more successful. The bacteria in this class 7 are, throughout the oceans, morphologically, biophysically and phylogenetically similar. These common features suggest that they represent a uniform class that has speciated from a common ancestor, presumably a purple non-sulfur bacterium. What differentiates this group from the previous four classes is that they metabolize organic carbon (they are thus heterotrophic) and use O2-dependent respiration (they are thus aerobic). When organic carbon is not available, they switch to photosynthesis. These microbes use light for the synthesis of organic matter but cannot use water as a reductant and do not produce O2. When light fails, they depend on the metabolism of organic carbon and other organic substrates to generate energy. The scholar, not necessarily pedant but because these are the correct terms to apply, will say that they are “obligatory aerobic anoxygenic facultative photoheterotrophs”. Their capacity to tap two widely different sources of energy provided them with a significant survival advantage over the phototrophs. The class is ubiquitous and represents about 11% of the total microbial community in the upper layers of the oceans.
It was assumed until 2002 that horizontal gene transfer from one species of bacteria to another would not be true for genes specifying complex processes as converting sunlight to biomass, which was presumably too complex to possibly coordinate for genes of a mixed ancestry. A comparison of the genomes of all the photosynthetic bacteria 8 indicates that these five (six if the purple bacteria are subdivided into two groups) share 200 genes. Among these, there are 50 photosynthesis genes. These genes moved from one bacterial species to another, to return later, but modified, to the original organism! Under these conditions, it is almost impossible to find the earliest ancestor for photosynthetic microbes, which are best all lumped together.
The most successful step taken towards a higher organizational level was accomplished by the still prokaryotic blue-green algae.
3.1.2 Blue-green, Red and Brown algae
The first organisms multiplying by cell division were little more than scavengers. Bacteria extract energy-rich compounds from the environment and release low-energy breakdown products. This anaerobic fermentation is part of our heritage. It is through this process that yeasts extract energy from sugar and release alcohol and also that muscle cramps occur when we over exercise and rapidly convert glucose into lactic acid.
The upper limit on how much life this planet could support with this anaerobic fermentation as the sole source of energy is then determined by the rate at which high-energy compounds are synthesized by physico-chemical means. In the long run, depletion in chemically produced glucose must have to some extent halted the wild proliferation of bacteria. They polluted their environment with ethanol, CO2 and other products of degradation while on the other hand they depleted their supplies.
A new system geared at synthesizing glucose from simpler precursors within the organism came into being. The life-carrying capacity of the earth increased tremendously when some organisms developed the ability to directly tap sunlight for energy. Some bacteria as well as the blue-green algae shared this ability. These algae were still very primitive in that their genetic material was not enclosed within a nucleus (fig.3.6).
Figure 3.6. Prokaryotic algae from the Gunflint cherts of Ontario dating 2 billion years ago are very diversified in form, even that early in time. "A" is a hydra-like form quite similar to an organism (Kakabekia) presently growing very slowly in ammonia rich soils. "B" may have a nucleus.
Plants synthesize a molecule of glucose from 6 molecules of CO2 and 6 molecules of water. At the end of the process, there is a surplus of oxygen atoms, which are released under the form of molecular oxygen, O2. This system continued on earth for such a long time that, starting with very little or no oxygen in the atmosphere, there is now an amount of oxygen making up 21% of it.
The main pigment of the blue-green algae (phycocyanin) enables the algae to absorb light very efficiently in the orange region of the spectrum. The restricted orange-red range of the spectrum exploited by the blue-green algae was due either to an intrinsic inability to devise mechanisms able to exploit broader ranges or more likely because these particular wavelengths were most abundant in those days when NH3, CO2 and H2O were decreasing the light penetration at both ends of the light scale.
Prokaryotic communities of blue-green algae are recorded in sedimentary structures known as stromatolites. The earliest finds bring the appearance of the blue-green algae back to about 1.6 to 2 billion years ago. The organisms found definitely possess the ability to produce oxygen, which is a capacity bacteria do not possess9. In the earliest times, they are already present under a very differentiated form (see fig.3.6), which they still have today. The morphological conservatism of these organisms is very great. There is some scant evidence that at least one species existing by that time was eukaryotic.
The prokaryotic blue-green algae are able to extract CO2 very efficiently from the surrounding environment. This would lend support to the view that these algae evolved in parallel with bacteria at the time when these bacteria began to release CO2 as a breakdown product of glucose metabolism. The atmosphere and waters must thus have passed through an initial stage where NH3 and H2 were mostly available with water vapor. This would thereafter have given way to an atmosphere devoid of NH3 but still with large amounts of water vapor and also CO2. This carbon dioxide was finally replaced by oxygen, which had the effect to substantially decrease the temperature, reduce water vapor in the atmosphere and favor the appearance of an ozone layer in the stratosphere.
The evolution of the blue-green algae was by no means simple and straightforward10. The protocyanobacteria that appeared about 3.5 billion years ago were planktonic populations. These populations needed visible light (orange) to prosper but, in the mean time, were subject to destruction by ultraviolet light. The ultraviolet light can be arbitrarily subdivided into light of wavelength below 280 nanometers (nm: a thousand millionth of a meter, 10-9 meters), which destroys the DNA through direct hits, light of wavelength between 280 and 320 nm, which destroys also directly the DNA and, in addition, uses activated oxygen to destroy additional proteins, and finally the wavelengths above 320 nm, which destroy essentially the proteins via molecular oxygen activation. In early days, there was no oxygen (it was present in the atmosphere at a concentration 10-14 compared to present levels), and thus played no role.
Primitive blue-green algae, in the Archaean eon (>2 billion years), were heavily exposed to UV light, with DNA damage about 44 fold greater than at present. This precluded any attempt at colonization of dry lands and forced the algae deep into the water. In the early Archaean, the low amounts of oxygen produced were taken up in near totality by reduced iron and the natural waters contained large amounts of dissolved iron sulfate (FeSO4) that afforded a substantial shield to deadly UV light. The transparency of the waters increased, due to the precipitation of the insoluble oxidized iron minerals, which fell to the bottom, where they again provided a shield against UV light but, in the mean time, the water became permeable to the UV light, around 1.9 billion years ago. As a result, the blue-green algae were evacuated from the seas but could survive as stromatolites at shallow depths, in evaporitic environments and intertidal ranges, under the protection of a blanket of minerals. At some point during the Archaean, true cyanobacteria appeared, able to use water as an electron donor in the making of oxygen.
During 500 million to 1000 million years, the true cyanobacteria produced oxygen. For the first time during evolution, UV radiation of long wavelength between 320 and 400 nanometers, which penetrates deeper into water and sediments than short wave radiations do but which also is much more abundant in the solar spectrum (remember that the solar radiations have increased by 30% during that time), became injurious. During these 500-1000 million years, both oxygen and deadly long wave UV light acted together on the algae, with an ever increasing stress on both DNA (by direct hits) and proteins (by activated oxygen), until finally the oxygen concentration in the atmosphere reached 1% of the present level, which allowed the formation of an ozone layer.
Survival of early cyanobacteria outside growth-limiting UV refuges must thus have been a long odyssey for which optimization of all available preventive and defense mechanisms was needed. Possibly, new devices were elaborated. The long time needed to reach a good level of oxygenation was perhaps due to these new requirements. With a good oxygenation, the flux of UV radiation reaching the ground progressively diminished and new habitats (soil surfaces, rocks) could be colonized.
The next more evolved algae are red, containing a phycoerythrin pigment. These algae and all the subsequently appearing algae are not the direct descendants of the blue-green algae but evolved from eukaryotic cells, that appeared at that moment. What they inherited from the blue-green algae was the photosynthesizing mechanism.
The maximum absorption of phycoerythrin lies in the blue light. Contrary to blue-green algae, the red algae are not living in surface waters but at depths of between 30 and 120 meters, where blue light of 525 millimicrons (another way to express a unit of 10-9 meters) still penetrates (fig.1.12). Some red algae live at depths of -268 meters, where only 0.0005 % of solar light penetrates. These algae require a high temperature to live and are mostly restricted to tropical waters. One may assume that they appeared before the first ice age, when waters were still warm, even hot. The brown algae live between 5 and 30 meters in the ocean waters.
The subsequent increase in oxygen and thus ozone may have rendered thereafter life near the ocean’s surface more bearable to eukaryotic cells and the well evolved green algae now live close to the surface. These green algae extract CO2 from the environment with such a high efficiency that 200 billion tons of carbon are fixed each year in the upper layers of the oceans. The release of oxygen in the atmosphere, producing in the meantime a cooling down of the earth and an efficient protection against UV light, allowed the passage of photosynthetic eukaryotes from water to land and also prompted an efficient utilization of this oxygen now available, through respiration in mitochondria. The cooling down was also propitious for the accumulation of organic material: below a temperature of 15°C, the decomposition of organic matter by most bacterial species is drastically inhibited. Furthermore, the development of cyano-bacterial communities is also dependent on dark-light variations. In those days, oxygen was still rare but nitrogen was abundant. At day-break, energy is available and blue algae assimilate it while, at night, the absence of available oxygen and light favors the activity of anaerobic bacteria, which partially decompose the lipids of the cellular membranes of the algae, that become a source of organic matter for kerogen.
Blue-green algae released a corrosive gas, i.e. oxygen. This increase in oxygen was not instantaneous. The slow augmentation of this gas resulted in a selective pressure and many organisms adapted to it, becoming aerobic or at least tolerant to the presence of oxygen. A predatory prokaryotic animalcule evolved, characterized by the fact that it possessed enzymes able to split up the chemical bonds of proteins, i.e. hydrolases. These hydrolases are stored in subcellular particles called lysozomes. Lysozomes are indeed present now in cells of green plants, in cells of animals, in cells of sponges and even in cells of green algae. The green algae would have thus as a father a prokaryotic animal cell that acquired only in later times its chloroplasts and chlorophyll. A hydra-like organism has been isolated in Alaska, Hawaii, Wales and Iceland, which contains no nucleus and no chlorophyll and grows very slowly in ammonia-rich soils. It may be a remnant of the original prokaryotes that drifted away from the bacteria about 2 billion years ago (see fig. 3.6).
This hypothesis is sustained by the fact that the protein synthesizing mechanism of the eukaryotes is complex and flexible. This complexity must have been also a characteristic present in paleobacteria. Eubacteria would then have evolved in simplifying the system (see fig. 3.1). The paleobacteria, after their repression due to a rising oxygen pressure and the exhaustion of nutritive supplies, would have had the chance to evolve in the eukaryotic direction, banking on the flexibility of their protein-synthesizing mechanism, which they maintained ever after. That such a hypothesis is plausible is shown by the fact that the gene of a virus inducing leukemia in fowl is found also in paleobacteria and also in the normal genetic stock of all vertebrates, including man. Also, the enzymes responsible in archeobacteria for the synthesis of messenger RNA’s are similar to those of the eukaryotes and different from those of the eubacteria.
6. Purple sulfur bacteria, purple non-sulfur bacteria, green sulfur bacteria and green non-sulfur bacteria. Other scholars acknowledge only three groups: proteobacteria (purple bacteria), green sulfur bacteria and green filamentous bacteria.
9. The accumulation of undecomposed organic matter in tropical swamps is due to the depletion of oxygen. In a closed system, the rapid consumption of organic matter causes oxygen deficiency. In the absence of external supplies of oxygen, the decomposition comes to a halt, with the accumulation of kerogen.