The relationship between the three domains of life. We have followed the original proposal and terminology used by Carl Richard Woese and co-workers, where the nucleated cells are grouped in the domain Eucarya, while the microorganisms themselves are called eukaryotes (Woese et al., 1977). 

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... the previous section we have sketched some of the most ancient microbes lying deepest at the root of the tree of life. We proceed to discuss briefly how the evolution of the Earth atmosphere repressed these Archaea into distinct niches. The main driving force was the gradual oxygenation of the atmosphere after the discovery of photosynthesis. Ecosystems adopted a layered mat-morphology and sediments. Such ecosystems are well known in present day environments, such as the dry valley lakes of Antarctica. The microbial mats found today in these environments are composed primarily of cyanobacteria, heterotrophic bacteria, protozoan cysts, eukaryotic algal cells and minerals associated with microbial activity occurring throughout much of the benthic regions of the dry valley lakes (Wharton et al., 1983; Mikell et al., 1984; Vincent, 1988). In the Archean the photosynthesizers were distributed in the upper layers, while the anaerobic microorganisms, such as the sulfate-reducing Archaea were relegated to the lower layers. The eventual consequence of this atmospheric factor was not only to segregate the sulfate reducers (and others such as the methanogens) to lower layers of the mat formations, but to these microorganisms were further relegated to restricted niches. Consequently it was inevitable that evolutionary diversification would follow. Indeed, today we have a large number of obligate anaerobes, not only Archaea, but also mesophilc bacteria. The microfossil record testifies that as oxygenation was gradually driven towards PAL by ~2.1 Ga BP, sulfate reducers and methanogens left their imprint supporting the general outline of Darwinian evolution of the three main domains of the tree of life (Fig. 1). Beyond the consequences of natural selection and adaptation, a new force in evolution, symbiosis, emerged that was to play a crucial role in the eventual dichotomy of multicelullar life: plants and animals as we shall discuss in the following ...

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... may separate living organisms in two large groups: prokaryotes (Bacteria and Achaea) and eukaryotes (Encarta, cf., Fig 1 and Sec. 2.2), the first group consists exclusively of unicellular organisms, considered vegetal organisms since immemorial times (Gerona, 1988) and the second, on the contrary, consists of all multicultural plants and animals inhabiting the Earth. On the base of this division we assume that bacteria and unicellular algae, in their quality of autotrophic organisms are considered vegetal organisms, and we focus our attention on the importance of the interactions of these organisms among themselves, with eukaryotes, and with the multicultural organisms. Frequently these interactions have developed along the history of life a sort of dependence, which very often comes into a real co-evolution for both organisms. The interactions between unicellular autotrophic organisms among them, and between prokaryotes and eukaryotes (unicellular and multicultural), play a major role in speciation and evolution. In general, the close ecological relationship between the individuals of two (or more) different species is defined as symbiosis. Ecologists use a different term for each type of symbiotic relationship: mutualism is defined as the symbiotic relationship between the individuals of two (or more) different species, where both species benefit; commensalisms implies only one of the interacting species benefits, the other is unaffected; finally, parasitism consists in one species benefits as the other remaining harmed. Microbial symbiosis is known today to be a ubiquitous aspect of life. According to contemporary conceptual consensus, the mitochondria of all eukaryotic cells and the chloroplasts of plants and protests were once free-living bacteria (alpha- proteobacteria and cyanobacteria, respectively) that became incorporated in a primitive host cell (Gray, 1992; Margulis, 1992). It was first suggested that chloroplasts originated as symbionts (Schimper, 1883). The concept was further developed by Merezhkowsky (Sapp , 2005), who coined the word “symbiogenesis” for such a synthesis of new organisms. He maintained that nucleus and cytoplasm had originated by symbiogenesis. Microbial evolutionists also consider whether the cell nucleus may have also arisen by some sort of fusion of symbiosis between two different kinds of bacteria. Neodarwinism considers the Cambrian explosion as the “big bang” of biology. During this period, between 560 and 495 Ma BP, many now-extinct plants and animals burst onto the scene. Why the Cambrian explosion occurred is not fully understood, but at the cellular scale the real “big bang” for plants and animals occurred some 1800 Ma earlier, with the first appearance of eukaryotic cells (Sapp, 2005). With its membrane- bound nucleus and all the associated features, such as mitosis, meiosis, and multiple chromosomes to package tens of thousands of genes per cell, it provided the material and the conditions for the differentiation of tissues, organs, and organ systems of plants and animals. Symbiosis is at the foundation of our being. Multicellular organisms, humans included, probably evolved and were maintained by bacteria. Symbiosis has not only played a principal role in the emergence of eukaryotes, it has been vital throughout eukaryote evolution. Although eukaryotes are the most morphologically complex microbes with the largest biomass on earth, have the greatest biochemical complexity (Whitman et al., 1998). Microbial symbionts perform many chemical reactions that are not possible for their hosts. Collectively they can photosynthesize, fix nitrogen, metabolize sulfur, digest cellulose, synthesize amino acids, provide vitamins and growth factors, and ward off pathogens. The fact that microbial symbiosis is a fundamental aspect of life was first suggested by botanists of the late 19 th century. The dual nature of lichens, nitrogen-fixing bacteria in the root nodules of legumes, fungi in the roots of forest trees and orchids, photosynthetic algae living inside the bodies of protists, hydra, and the flat worm Convoluta roscoffensis, suggested a temporal continuum of dependency of microbe and host from transient to permanent interdependence. When these phenomena were considered together with cytological evidence for reproducing organelles within the cells of plants and animals, they led several biologists of the late 19 th century to a conception of the cell itself as a symbiotic community (Sapp, 1994). Speciation induced by parasitic or mutualistic symbionts has been suggested for taxa ranging from plants to insects to monkeys (Thompson, 1987). Models for symbiont-induced speciation have been proposed based upon hybrid inferiority and selection for reinforcement genes. However, taken on their own, such models have severe theoretical limitations and little empirical support. Thompson highlighted the importance of the environment on the symbiont- induced speciation. He established two conditions for symbiont-induced speciation: firstly, interaction norms in which the outcomes of ...

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... dichotomy between plants and animals evolved from the microbial world that lasted for the major part of Earth’s history (Archean and Proterozoic). The microbial cellular plan consists of prokaryotes, lacking a central nucleus and eukaryotes that evolved later containing a central nucleus enveloping the genetic material. Eukaryotes were earlier considered similar to eubacteria and archaeobacteria and diversified from a universal last common ancestor (Fig. 1). In the Archean biosphere, the microbial communities were dominantly marine, however, unicellular eukaryotes must have been present. The unicellular organisms that can survive in extreme conditions are very close to the eukaryotes evolved in Paleoproterozoic around 2.1 billion years (Ga) before the present (BP). Cyanobacteria were the main prokaryotic microbial fossils reported from rocks dating from 3.5 Ga BP. Life on Earth has been classified in three domains Archaea, Bacteria and Eucarya (eukaryotes), (Woese et al., 1990). The evolution of eukaryotes is a debatable subject. The Archean oceans may have colonized by prokaryotes and proto-eukaryotes. The prokaryotes are single-celled microorganisms and can be easily distinguished by their DNA structure that is simple and not bounded by membrane and nucleus. The mitochondria, chromosomes and chloroplasts are also lacking in prokaryotic cells. The symbiosis between prokaryotes and eukaryotes resulting in modern mitochondria and chloroplasts are well established. This remark lies at the basis of the eventual separation of multicellular organisms between plants and animals (cf., Sec. 3.1). It is believed that the modern eukaryotic cell resulted from symbiosis of eubacterial organelles into an Archaea-like rootstock (Margulis and Cohen, 1994). The Archaea domain includes, amongst others, hot spring bacteria and methanogens. The Bacteria domain includes cyanobacteria, anoxygenic photosynthetic bacteria and the mitochondria and chloroplasts of the eukaryotes (Wheelis et al., 1992). Archaea and Eucarya shared a common ancestor that was not shared by Bacteria. Hyperthermophiles diverged from the Archaea-Eucarya domains (Woese et al., 1990, Wheelis et al., 1992). Paleobiological evidence indicates that eukaryotes evolved more than 2 Ga BP. Modern unicellular organisms surviving in the extremely hot conditions may be their modern analogues (Tewari et al., 2008). This view differs from the earlier view that the eukaryotes share a common ancestry with Archaea. This evidence was based on genes that code for RNA of ribosomes in Eucarya, Archaea and Bacteria. The nuclear genome contains genes that are of specific eubacterial origin, and some genes are specific to eukaryotes (Woese, 1987). The first appearance of endosymbiont eukaryotes is not clear, however, they must have originated in late the Archean. Multicellular eukaryotes evolved later, around 1.5 - 1.0 Ga BP. These metazoans appeared as a major eukaryotic radiation in the Mesoproterozoic period around 1.0 - 0.8 Ga BP (Knoll, 1984). Terminal Neoproterozoic (0.65-0.57 Ga BP) was the time of Ediacaran explosion of diploblastic animals (Conway Morris, 1989; Narbonne and Hofmann, 1987). Their possible modern analogues are coelenterates like jellyfish, corals and sea anemones. The Cambrian explosion of triploblastic animals with three germ layers is the major event of multicellular metazoans. In the present paper we discuss physical and paleobiological evidences of prokaryote to eukaryote evolution on Earth. The presence of microorganisms in Antarctic lakes including eukaryotic diatoms and cyanobacteria not only supports the idea that life can survive in extreme environments, but also that life may thrive on Mars and Europa (Chela Flores 1998; Chela Flores et al., 2008; Tewari, 1998, ...

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... closer and more detailed understanding of the origin of life on Earth has forced upon us a more significant view on the Late Archean and Early Proterozoic evolution of trophic relations in the microworld. Presently we are more aware that hydrothermal vents in the Earth oceans may have played a role in the origin and evolution of the three domains of life (cf., Fig. 1). Indeed, it is possible that throughout evolution entire ecosystems depend on geothermal, rather than solar energy. This is not only evident on the Earth, but this is also likely to be the case on the other oceans of the solar system, as for example on the moons of Jupiter: Europa and Ganymede. On these satellites this particular hypothesis for the origin of life may be tested in the foreseeable future. The Europa-Jupiter System Mission is now being seriously considered by the main space agencies of Europe, the United States, Japan and Russia, after the initial proposal of the LAPLACE mission (Blanc et al., 2009). The primary sources of organic matter for the microbial autotrophs are photosynthesis, methanogenesis and sulfate reduction. In the limited space available it is most important to single out and highlight that the group of sulfate reducers may contain some of the earliest forms of life on Earth. Thus, this special form of metabolism may hold the key to understanding the primordial state of life, since sulfate-reducers are in deeply rooted branches of the phylogenetic tree of life (Shen and Buick, 2004). The morphological simplicity of the primitive sulfate reducers is one drawback in probing the fossilized remains of these microbes. Instead we must rely on the science of biogeochemistry when our objective is to enquire on the antiquity of life and its trophic relations. From the early papers of Manfred Schildowski and co-workers the stable isotope geochemistry of sulfur and the other biogenic elements (H, C, O, N) has been reviewed extensively (Schildowski, 1983; Strauss and Beukes, 1996). For a proper understanding of the Archean S-isotopic record we should first realize that the abiotic fractionation of carbon isotopes can produce effects comparable to geomicrobiological effects, as described in detail elsewhere (Horita, 2005). However, the situation is more favorable for sulfur. Indeed, microorganisms mediate the reduction of sulfate to sulfide. The resulting fractionations can be reliably taken as good markers for the geological record, especially for the Archean S-isotopic record, where we have hinted that the oldest signatures for life are to be retrieved. The biology that underlies this significant aspect of our quest for the evolution of trophic relations is as follows: the preferential use of 32 S over 34 S by microorganisms deplete the sulfide in the environment of 34 S with respect to the original sulfate. Several species of bacteria and Archea can make this happen via the metabolic pathway known as dissimilatory sulfate reduction. Sulfur itself is not incorporated into cell, but it ends up in the oxidation of organic matter. In normal marine sediments of sulfate, the fractionation can range from 10 to 49 ‰, but this effect can be as large as 70 ‰. On the other hand, unlike the case of carbon described above, abiotic isotope fractionations can yield fractionations in the range 15- 20 ‰, for example in the magmatic reduction of gaseous sulfate to hydrogen sulfide (Rollinson, 2007). This leaves an ample margin for distinguishing the microbial activity in rocks at a hydrothermal vent and the abiotic fractionations. The S-isotopic record of sulfide and sulfate in Archean sedimentary rocks ranges from Isua of ~3.8 Ga BP (pyrite in banded-iron formations) and ~3.47 Ga BP (barite deposits). In these early times the sulfate reducers were beginning to leave measurable traces, but some difficulties have still to be fully understood, as to their sources and the role of the atmospheric contributions. In the more recent pyrites in black shales of ~2.7 Ga BP (Shen and Buick, 2004, Fig. 6), where the traces are better understood. In conclusion the stable isotope geochemistry of the ~3.47 Ga barite deposit suggests that reactions mediated by microorganisms were already fractionating sulfur much in the same way as present day sulfate-reducing ...