From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya

The theory of a chemoautotrophic origin of life in a volcanic iron-sulphur world postulates a pioneer organism at sites of reducing volcanic exhalations. The pioneer organism is characterized by a composite structure with an inorganic substructure and an organic superstructure. Within the surfaces of the inorganic substructure iron, cobalt, nickel and other transition metal centres with sulphido, carbonyl and other ligands were catalytically active and promoted the growth of the organic superstructure through carbon fixation, driven by the reducing potential of the volcanic exhalations. This pioneer metabolism was reproductive by an autocatalytic feedback mechanism. Some organic products served as ligands for activating catalytic metal centres whence they arose. The unitary structure-function relationship of the pioneer organism later gave rise to two major strands of evolution: cellularization and emergence of the genetic machinery. This early phase of evolution ended with segregation of the domains Bacteria, Archaea and Eukarya from a rapidly evolving population of pre-cells. Thus, life started with an initial, direct, deterministic chemical mechanism of evolution giving rise to a later, indirect, stochastic, genetic mechanism of evolution and the upward evolution of life by increase of complexity is grounded ultimately in the synthetic redox chemistry of the pioneer organism.     

早期地球的环境变化和生命的化学进化

生命起源是当代最大的科学疑谜之一,也是历来人类普遍关注的一个焦点。在地球上最早的生物出现之前,有机物经历了漫长而复杂的化学进化过程,称为生命的化学进化。地球上生命的化学进化与非生物部分的早期演化过程,是密切地相互关联、相互作用并相互制约的。文章着重阐述与生命的化学关系最为密切的冥古宙和太古宙的地球演化历史,指出这两个阶段所形成的还原性原始大气和古海洋条件在生命的化学进行中起了极其重要的作用,并且从宇宙形成、太阳系演化和地球环境早期演化的角度,探讨地球生命的化学进化历程;以地球形成初期发生了一系列复杂的有机化学反应过程,由无机分子生成生物小分子,再进一步生成生物大分子,直至最后产生原始细胞。此外,文章评述当前国际上最流行的生命化学进化学说,对早期地球的化学进化是发生在地球表面的原始海洋、粘土矿物、火山喷发等,或是来源于地球之外的宇宙空间进行了综合的阐述。     

The fundamental nature of life as a chemical system: the part played by inorganic elements

In this article we show why inorganic metal elements from the environment were an essential part of the origin of living aqueous systems of chemicals in flow. Unavoidably such systems have many closely fixed parameters, related to thermodynamic binding constants, for the interaction of the essential exchangeable inorganic metal elements with both inorganic and organic non-metal materials. The binding constants give rise to fixed free metal ion concentration profiles for different metal ions and ligands in the cytoplasm of all cells closely related to the Irving-Williams series. The amounts of bound elements depend on the organic molecules present as well as these free ion concentrations. This system must have predated coding which is probably only essential for reproductive life. Later evolution in changing chemical environments became based on the development of extra cytoplasmic compartments containing quite different energised free (and bound) element contents but in feed-back communication with the central primitive cytoplasm which changed little. Hence species multiplied late in evolution in large part due to the coupling with the altered inorganic environment.     

A Suggested Pioneer Organism for the Wächtershäuser Origin of Life Hypothesis

A suggested pioneer organism for the Wächtershäuser origin of life hypothesis is presented. In this scenario, a cubic pyrite crystal edge serves as a catalytic surface for the production of a proto-nucleic acid. Computational analysis demonstrates how the vacant cubic pyrite edge could be populated by iron(II) and hydrogen phosphate, capped with a distorted iron pentacarbonyl. A bridging iron sulfide then forms blocking one side of the edge. The carbonyl on the other side of the edge can then react with either existing uracil or cytosine, to produce a nitrogen-iron carbonyl intermediate. This intermediate serves as a free radical initiator for a polymerization of carbon monoxide and molecular hydrogen. After the fourth carbon is added to the chain, the polymerization is terminated by ring formation yielding a condensed ribose. The resultant product is a proto-nucleic acid, a pioneer organism.     

Abiogenic synthesis of prebiotic matter for the Earth’s biosphere as a stage of self-organization on an astrophysical and paleontological time scale

Existing data suggest that an early circumstellar preplanetary disk was the most likely location for primary abiogenic synthesis of prebiotic organic matter from simple molecules along with the “RNA world” and the origin of life. This paper discusses the stages of self-organization that have resulted in the Earth’s modern biosphere, and the relationships between astrophysical and paleontological events in evolution.     

The evolution of photosynthesis…again?

‘Replaying the tape’ is an intriguing ‘would it happen again?’ exercise. With respect to broad evolutionary innovations, such as photosynthesis, the answers are central to our search for life elsewhere. Photosynthesis permits a large planetary biomass on Earth. Specifically, oxygenic photosynthesis has allowed an oxygenated atmosphere and the evolution of large metabolically demanding creatures, including ourselves. There are at least six prerequisites for the evolution of biological carbon fixation: a carbon-based life form; the presence of inorganic carbon; the availability of reductants; the presence of light; a light-harvesting mechanism to convert the light energy into chemical energy; and carboxylating enzymes. All were present on the early Earth. To provide the evolutionary pressure, organic carbon must be a scarce resource in contrast to inorganic carbon. The probability of evolving a carboxylase is approached by creating an inventory of carbon-fixation enzymes and comparing them, leading to the conclusion that carbon fixation in general is basic to life and has arisen multiple times. Certainly, the evolutionary pressure to evolve new pathways for carbon fixation would have been present early in evolution. From knowledge about planetary systems and extraterrestrial chemistry, if organic carbon-based life occurs elsewhere, photosynthesis—although perhaps not oxygenic photosynthesis—would also have evolved.     

Oxygenic photosynthesis–a photon driven hydrogen generator–the energetic/entropic basis of life

Photosynthesis, as a fundamental element in the life process, is integrated in the evolution of living systems on the basis of hydrogen cycles on various hierarchic levels. Conversion of radiant energy enables the oxidation of water, whereby free oxygen accumulates in the atmosphere. Hydrogen is (reversibly) stored in organic materials formed under reductive CO2-fixation and by the incorporation of the other elements, which are necessary for living systems. All endergonic processes in living cells are finally driven by the energy released through the clean recombination of protons and electrons with oxygen to water. Duration of the stored energy and the complexity of the systems thus produced is correlated negatively with the conversion efficiency of the radiation energy. Entropy is a unifying principle in the evolution of living systems, inclusive human societies.     

The evolution of calcium biochemistry

The role of calcium in evolution is best understood from a perspective based on its intrinsic value as a divalent cation able to bind and precipitate inorganic and organic anions rapidly. This binding can be useful or inhibitory. Now treatment of binding or precipitation has two different interests in biological cells. The first is thermodynamic, that is the stress is on systems biology and the second is structure, that is molecular biology. In evolution both have equal weight being connected through exchange. This paper outlines first the systems biology of the evolution of calcium functions from prokaryotes to animals with brains. The calcium ion was the only good available candidate in the environment for the functions it performs. The second section of the paper describes the evolution of the proteins which allow the messenger function. We have discussed elsewhere the structure/function relationships of the proteins. Overall the evolving and increasing involvement of calcium as possibly the major control messenger of events outside cells to action inside them is an inevitable feature of the nature of ecological, that is environmental/organism, evolution.     

Does life originate from a single molecule?

Life did not emerge in a single step. In chemical evolution, the first formation of a self-replicating molecule was probably one of the most critical bottlenecks, which was overcome only with a very low probability. If only one such event was successful, present-day life originates from a single molecule. In this case, homochirality in DNA and RNA is explained almost without further assumptions. By contrast, the enantiomer excess, produced by the deterministic mechanisms suggested so far, is smaller than the statistical standard deviation, unless the postulated initial number of molecules is very--in some mechanisms unreasonably--large. A certain chiral nonuniformity of natural monosaccharides other than (deoxy)ribose supports the idea that homochirality originates not from such small molecules but from an early RNA-like oligomer. This nonuniformity seems also hard to explain by any deterministic mechanism.     

Some Aspects of the Biology of Fusarium oxysporum Schl. in Soil

From either a mycelial or a conidial inoculum the fungus survivedin soil as inactive chlamydospores. The level of its soil populationat equilibrium was too low to be studied by dilution plating.Plant materials placed on or beneath the surface of inoculatedsoil were colonized deeply by the fungus, which produced conidiaon them. Dispersal of conidia can occur with water movementin soil, and at right angles to, as well as in the directionof, that movement. No evidence was found of dispersal of thefungus in soil by continuous growth, even over continuous stretchesof organic matter. This finding was related to the inabilityof the fungus to colonize those organic materials that werepreviously colonized by other organisms from the soil, unlessits inoculum potential were greatly augmented. The fungus isthus seen to be a pioneer fungus. The strain used here grewoutwards a short distance from colonized organic food basesin the soil, leaving in the soil resting spores which couldcolonize fresh pieces of organic material subsequently addedthere. The organism could thus spread by discontinuous growthon successively available, fresh, organic materials.     

Some Aspects of the Biology of Fusarium oxysporum Schl. in Soil

From either a mycelial or a conidial inoculum the fungus survivedin soil as inactive chlamydospores. The level of its soil populationat equilibrium was too low to be studied by dilution plating.Plant materials placed on or beneath the surface of inoculatedsoil were colonized deeply by the fungus, which produced conidiaon them. Dispersal of conidia can occur with water movementin soil, and at right angles to, as well as in the directionof, that movement. No evidence was found of dispersal of thefungus in soil by continuous growth, even over continuous stretchesof organic matter. This finding was related to the inabilityof the fungus to colonize those organic materials that werepreviously colonized by other organisms from the soil, unlessits inoculum potential were greatly augmented. The fungus isthus seen to be a pioneer fungus. The strain used here grewoutwards a short distance from colonized organic food basesin the soil, leaving in the soil resting spores which couldcolonize fresh pieces of organic material subsequently addedthere. The organism could thus spread by discontinuous growthon successively available, fresh, organic materials.     

Metal sulfides in oxygenated aquatic systems: implications for the biotic ligand model

The Biotic Ligand Model (BLM) attempts to predict metal toxicity to aquatic organisms on the basis of metal speciation and effects at the cell surface. Current versions of the BLM for silver and copper consider metal binding by inorganic ligands, dissolved organic matter (DOM) and also competition at the cell surface from calcium and protons (pH). Recent studies reported in the geochemical and ecotoxicological literature have indicated the importance of sulfide as a ligand, even in fully oxygenated aquatic systems. Speciation calculations for oxygenated waters do not currently include reduced sulfur as a ligand and as a consequence, no version of the BLM model has been published including reduced sulfur. This reflects the limitations on our knowledge regarding reduced sulfur in aquatic systems. In this paper we highlight the need to include reduced sulfur in the Biotic Ligand Model, with the interaction between silver and inorganic metal sulfides as a specific example. The geochemical importance of metal sulfides as ligands for silver and the effect of 'dissolved' metal sulfide and other ligands on metal toxicity and accumulation are described and reviewed. Recommendations are made for future work needed to incorporate sulfide ligands into the BLM's modeling framework.     

Evolution of proton pumping ATPases: Rooting the tree of life

Proton pumping ATPases are found in all groups of present day organisms. The F-ATPases of eubacteria, mitochondria and chloroplasts also function as ATP synthases, i.e., they catalyze the final step that transforms the energy available from reduction/oxidation reactions (e.g., in photosynthesis) into ATP, the usual energy currency of modern cells. The primary structure of these ATPases/ATP synthases was found to be much more conserved between different groups of bacteria than other parts of the photosynthetic machinery, e.g., reaction center proteins and redox carrier complexes.These F-ATPases and the vacuolar type ATPase, which is found on many of the endomembranes of eukaryotic cells, were shown to be homologous to each other; i.e., these two groups of ATPases evolved from the same enzyme present in the common ancestor. (The term eubacteria is used here to denote the phylogenetic group containing all bacteria except the archaebacteria.) Sequences obtained for the plasmamembrane ATPase of various archaebacteria revealed that this ATPase is much more similar to the eukaryotic than to the eubacterial counterpart. The eukaryotic cell of higher organisms evolved from a symbiosis between eubacteria (that evolved into mitochondria and chloroplasts) and a host organism. Using the vacuolar type ATPase as a molecular marker for the cytoplasmic component of the eukaryotic cell reveals that this host organism was a close relative of the archaebacteria.A unique feature of the evolution of the ATPases is the presence of a non-catalytic subunit that is paralogous to the catalytic subunit, i.e., the two types of subunits evolved from a common ancestral gene. Since the gene duplication that gave rise to these two types of subunits had already occurred in the last common ancestor of all living organisms, this non-catalytic subunit can be used to root the tree of life by means of an outgroup; that is, the location of the last common ancestor of the major domains of living organisms (archaebacteria, eubacteria and eukaryotes) can be located in the tree of life without assuming constant or equal rates of change in the different branches.A correlation between structure and function of ATPases has been established for present day organisms. Implications resulting from this correlation for biochemical pathways, especially photosynthesis, that were operative in the last common ancestor and preceding life forms are discussed.     

Oxygen evolution and the permeability of the outer envelope of isolated whole chloroplasts

A rapid oxygraph method of studying the permeability of the envelope of isolated chloroplasts was used. The outer envelope of aqueously isolated whole spinach (Spinacia oleracea L.) chloroplasts in buffer is readily permeable to 3-phosphoglyceric acid, which induces an immediate light dependent oxygen evolution. This light dependent oxygen evolution was completely eliminated by swelling these plastids in an osmotically dilute solution. Exogenous adenosine diphosphate, but not inorganic phosphate, strongly stimulated this oxygen evolution. This indicated that the chloroplast envelope is relatively permeable to adenosine diphosphate.

Oxygen evolution and swelling studies indicated that the chloroplast envelope is relatively impermeable to NADP and to ferredoxin.

A method is described whereby the percent of whole chloroplasts present in a chloroplast preparation may be rapidly estimated.

     

Historic and functional biology: the inadequacy of a system theory of evolution

In the first half of the 20th century neo-Kantianism in a broad sense proved itself the main conceptual and methodological background of the central European biology. As such it contributed much to the victory on the typological, idealistic-morphological and psycho-vitalistic interpretations of life. On the other hand it could not give tools to the biologists for working out a strictly darwinian evolution theory. Kant's theory of organism was conceived without evolution as a theory of the internal functionality of the organism. There was only some 'play' with the evolutionary differentiation of the species. Since then the disputes around the work of August Weismann, a synthetical evolution theory which is now behind time, arose. This theory developed from coinciding claims, elaborated by geneticists, mathematicians, and by biologists studying development, natural history and systematics. This was done under a strong influence of marxist ideas. Through the interweaving of such different approaches it was possible for this evolutionary synthesis to influence successfully the development of evolution research during more than 40 years. Philosophically speaking modern evolution theory means therefore an aversion, even a positive abolition of Kantian positions. A number of biologists however--as L. von Bertalanffy--refused to adhere to a misinterpreted Kantian methodology and oriented themselves to an approach via system theory, which obtained a place in evolution research. In fact this is a Kantian approach as well. They only repeated the Kantian dilemma of the evolution which can also be found in Lamarck and Hegel. The system theory of the functionality of the organism never reaches to the level of the evolving species, but remains always on the level of epigenetic thinking, because of its philosophical origin. This paper points out the consequences of this still current dilemma. At the same time an all-enclosing reflection on the methodological, epistemological and the important historical questions of evolutionary biology in its scientific context is recommended.     

The obligate autotroph — the demise of a concept

Autotrophy is a life style in which inorganic compounds provide for all nutritional needs of an organism. Implicit in this definition is the capacity of an organism to derive all cell carbon from CO₂ and to obtain ATP either photosynthetically or chemolithotrophically. The existence of bacteria with such potentials has been known since the work of Winogradsky in the 1880's. The question explored in this paper is whether bacteria exist that must of necessity live autotrophically, i.e., the obligate autotrophsensu Winogradsky. The evidence is briefly reviewed and leads to four conclusions. One: there is no obligatory coupling between phototrophy and autotrophy or between chemolithotrophy and autotrophy. Two: autotrophic bacteria are not uniquely inhibited by organic matter. Three: all putative obligate autotrophic bacteria so far tested assimilate and metabolize exogenously supplied organic compounds. Four: mixotrophy can exist with respect to autotrophic and heterotrophic biosynthetic mechanisms and/or to chemolithotrophic and chemoorganotrophic energy-generating processes. Examples remain of bacteria that have not been cultured in the absence of an inorganic energy source or light. Such forms are appropriately described as obligate chemolithotrophs or obligate phototrophs. The available evidence, briefly categorized above, suggest that none of these bacteria is, at the same time, an obligate autotroph. From ecological and evolutionary considerations, an absolute dependence on carbon dioxide for all carbon makes little sense, and bacteria with such a requirement would be an anachronism on earth as it now exists. A lecture delivered before the third meeting of the Northwest European Microbiological Group, on August 18, 1971 at Utrecht, the Netherlands. The work reported from the author's laboratory was supported by grants from the National Science Foundation.     

Utilization of Glucose and the Effect of Organic Compounds on the Chemolithotroph Thiobacillus ferrooxidans

The utilization of glucose by the chemolithotroph Thiobacillus ferrooxidans results in a repression of the ability to oxidize iron, the substrate for autotrophic growth. An assay with resting cells was used to measure iron oxidation rates. Concomitant with the decreased iron oxidation rates, the enzyme responsible for carbon dioxide fixation, ribulose diphosphate (RuDP) carboxylase, was also repressed. Maximum iron oxidation rates precede peak RuDP carboxylase levels, consistent with the role of these processes in autotrophic metabolism in nonrepressed cells. The degree of iron oxidation repression depends on the organic substrate supplied, as does the level of RuDP carboxylase. The uptake of glucose parallels an increase in synthesis of glucose-6-phosphate dehydrogenase and the accumulation in cells of poly-beta-hydroxybutyrate. The organism is also capable of growing on glucose and other organic supplements in the absence of its inorganic energy source; growth rates depend on the organic substrate supplied.     

Effect of ligands and other metals on the uptake of mercury and methylmercury across the gills and the intestine of the blue crab (Callinectes sapidus)

Using the perfusion method, we compared the accumulation and flux of inorganic mercury (Hg) and methylmercury (CH(3)Hg) across the gills and intestine of the blue crab, Callinectes sapidus. The accumulation and transfer processes were studied for each form by exposing the organs in the presence of specific ligands and other metals. While binding of Hg and CH(3)Hg to organic ligands reduced the rate of uptake in most instances, the differences in accumulation could not be explained only in terms of passive diffusive uptake. Thus, it appears that Hg and CH(3)Hg accumulation is dominated by ligand exchange or facilitated transport processes. Exposure of the gills and intestine in the presence of a suite of metals and metalloids showed that inorganic Hg and CH(3)Hg uptake was largely by different mechanisms to that of the other elements, as there was little interaction in terms of uptake rate. Overall, the results of this study suggest that inorganic Hg and CH(3)Hg uptake into the gills and intestine of this invertebrate is by a variety of pathways, both active and passive.     

Adaptation to developmental diet influences the response to selection on age at reproduction in the fruit fly

Experimental evolution (EE) is a powerful tool for addressing how environmental factors influence life‐history evolution. While in nature different selection pressures experienced across the lifespan shape life histories, EE studies typically apply selection pressures one at a time. Here, we assess the consequences of adaptation to three different developmental diets in combination with classical selection for early or late reproduction in the fruit fly Drosophila melanogaster. We find that the response to each selection pressure is similar to that observed when they are applied independently, but the overall magnitude of the response depends on the selection regime experienced in the other life stage. For example, adaptation to increased age at reproduction increased lifespan across all diets; however, the extent of the increase was dependent on the dietary selection regime. Similarly, adaptation to a lower calorie developmental diet led to faster development and decreased adult weight, but the magnitude of the response was dependent on the age‐at‐reproduction selection regime. Given that multiple selection pressures are prevalent in nature, our findings suggest that trade‐offs should be considered not only among traits within an organism, but also among adaptive responses to different—sometimes conflicting—selection pressures, including across life stages.     

Controversies on the origin of life.

Different viewpoints, many with deep philosophical and historical roots, have shaped the scientific study of the origin of life. Some of these argue that primeval life was based on simple anaerobic microorganisms able to use a wide inventory of abiotic organic materials (i.e. a heterotrophic origin), whereas others invoke a more sophisticated organization, one that thrived on simple inorganic molecules (i.e. an autotrophic origin). While many scientists assume that life started as a self-replicative molecule, the first gene, a primitive self-catalytic metabolic network has also been proposed as a starting point. Even the emergence of the cell itself is a contentious issue: did boundaries and compartments appear early or late during life's origin? Starting with a recent definition of life, based on concepts of autonomy and open-ended evolution, it is proposed here that, firstly, organic molecules self-organized in a primordial metabolism located inside protocells. The flow of matter and energy across those early molecular systems allowed the generation of more ordered states, forming the cradle of the first genetic records. Thus, the origin of life was a process initiated within ecologically interconnected autonomous compartments that evolved into cells with hereditary and true Darwinian evolutionary capabilities. In other words, the individual existence of life preceded its historical-collective dimension.