On the early evolutionary stage of the geosphere and biosphere and the problem of early glaciations

The early evolutionary stages of the geosphere and biosphere are determined by three interrelated factors: (1) continuous cooling of the surface and interior (mantle) of the Earth (the mean temperatures of the mantle and surface decreased by a factor of 1.5–2 and 3–4, respectively; the mean heat flow was reduced by approximately one order of magnitude, and viscosity, by three orders); (2) continuous stepwise oxidation of the surface, which was particularly well pronounced from 3.8 to 1.8 Ga; and (3) periodic and correlated fluctuations of conditions in the geosphere and biosphere of varying extent and nature. The major boundaries of this evolution were about 4 Ga (the origin of rather thick and heterogeneous earth’s crust, the origin of life); about 3 Ga (appearance of a strong magnetic field, an increase in photosynthetic activity); about 1.8–1.9 Ga (appearance of an oxidized atmosphere, the first supercontinent, possibly, the first superplumes from the nucleus); and about 0.75 Ga (acceleration of subduction, “watering” of the upper mantle, elevation of continents with vast land masses, shelves, large rivers, and the first great glaciations). The significance and correlations of the earliest events (before and about 4 Ga) and events about 750 Ma are widely debated. In the Late Archean and Early Proterozoic (before 1.8 Ga), the biosphere was dominated by cyanobacteria, the dynamics and developmental peaks of which are marked by the presence of widespread stromatolite buildups in carbonaceous rocks (initially, mostly dolomitic matter). About 700–750 Ma, intense and frequent glaciations developed, marking the cooling of the Earth. The greatest glaciation apparently occurred about 640 Ma, which gave rise to the discussion of the model of the Snowball Earth. The emergence and evolution of skeletons in animals is sometimes thought to be connected with glaciations. These events are correlated and accounted for by great endogenous changes. One of the major events in endogenous history is the onset about 750 Ma of periodic manifestation of mantle flows (superplumes), which explain further periodicity of the biosphere evolution. In conclusion, extrapolation of future evolution and successive collapse of biosphere segments in the course of transformation of the Sun into a red star and warming of the Earth surface are proposed.     

Life conditions on the early Earth after 4.0 Ga

The organization level of Precambrian fossils is the most reliable indicator of the state and parameters of the biosphere, such as the atmosphere composition, average temperature of the earth’s surface, and others. At present, cyanobacteria, unicellular and multicellular eukaryotes, and coelomates are considered to appear in the geological history of the Earth much earlier than it was supposed previously. Our knowledge and ideas of the early Earth are very important for considering the problems of the origin of life. A key boundary of the earliest period was probably about 4 Ga. This boundary is between the periods documented and undocumented by the geological record. The Earth history and probable surface conditions before 4 Ga are considered by L.M. Mukhina, A.V. Vityazeva, G.V. Pechernikova, and L.V. Ksanfomaliti in this volume.     

Humic substances in the early biosphere

Humic substances and their organic-mineral compounds are the first stage in transformation of biotic residues into stable geopolymers, which comprise the main reservoir of organic C in the biosphere. Early appearance of HS in the Earth’s history is of principal importance for the understanding of geo-biological processes on land in the past. However, there is no fossil record of HS before land colonization by lignified vegetation (400 Ma). When the first soil HS were formed? Could HS be synthesized in the Precambrian before plants and mosses terrestrialization? The formation of HS occurs in mesophilic aerobic conditions and requires presence of oxidative catalysts and production of aromatic (phenolic) precursors by biota. In this paper, humification processes in algo-myco-bacterial and lichen communities are discussed from actualistic point of view. These communities are considered as a relict ecosystem, which could dominate on land during the Neoproterozoic-Early Paleozoic (1–0.5 Ga).     

Biogeochemical transformations after the emergence of oxygenic photosynthesis and conditions for the first rise of atmospheric oxygen

The advent of oxygenic photosynthesis represents the most prominent biological innovation in the evolutionary history of the Earth. The exact timing of the evolution of oxygenic photoautotrophic bacteria remains elusive, yet these bacteria profoundly altered the redox state of the ocean–atmosphere–biosphere system, ultimately causing the first major rise in atmospheric oxygen (O₂)—the so-called Great Oxidation Event (GOE)—during the Paleoproterozoic (~2.5–2.2 Ga). However, it remains unclear how the coupled atmosphere–marine biosphere system behaved after the emergence of oxygenic photoautotrophs (OP), affected global biogeochemical cycles, and led to the GOE. Here, we employ a coupled atmospheric photochemistry and marine microbial ecosystem model to comprehensively explore the intimate links between the atmosphere and marine biosphere driven by the expansion of OP, and the biogeochemical conditions of the GOE. When the primary productivity of OP sufficiently increases in the ocean, OP suppresses the activity of the anaerobic microbial ecosystem by reducing the availability of electron donors (H₂ and CO) in the biosphere and causes climate cooling by reducing the level of atmospheric methane (CH₄). This can be attributed to the supply of OH radicals from biogenic O₂, which is a primary sink of biogenic CH₄ and electron donors in the atmosphere. Our typical result also demonstrates that the GOE is triggered when the net primary production of OP exceeds >~5% of the present oceanic value. A globally frozen snowball Earth event could be triggered if the atmospheric CO₂ level was sufficiently small (<~40 present atmospheric level; PAL) because the concentration of CH₄ in the atmosphere would decrease faster than the climate mitigation by the carbonate–silicate geochemical cycle. These results support a prolonged anoxic atmosphere after the emergence of OP during the Archean and the occurrence of the GOE and snowball Earth event during the Paleoproterozoic.     

STUDY ON STROMATOLITIC DECLINE EVENT IN TERMINAL PRECAMBRIAN

In Precambrian, stromatolites, especially columnar stromatolites, underwent a marked evolutionary process from beginning of development through extensive flourish to rapid decline. The present paper makes a discussion on the exact data and cause of the stromatolitic decline in an attempt to reveal the evolution of biosphere and change of ecological environments in the terminal Precambrian according to a study of the stromatolitic decline event.     

On the early stages of the evolution of the geosphere and biosphere

The conditions necessary for the existence of nucleic-protein life are as follows: the presence of liquid water, an atmosphere, and a magnetic field (all of which protect from meteorites, abrupt changes in temperature, and a flow of charged particles from space) and the availability of nutrients (macro-and microelements in the form of dissolved compounds). In the evolution of the geosphere, complex interference of irreversible processes (general cooling, gravitational differentiation of the Earth’s interior, dissipation of hydrogen, etc.) with cyclic processes of varying natures and periodicities (from the endogenic cycles “from Pangea to Pangea” to Milankovitch cycles), these conditions have repeatedly changed; hence, in the coevolution of the geosphere and biosphere, the vector of irreversible evolution was determined by the geosphere. Only with the appearance of the ocean as a global system of homeostasis, which provided the maintenance and leveling of nutrient concentrations in the hydrosphere, and the conveyor of nutrients from the mantle, “the film of life” could begin its expansion from the source of the nutrients. Life itself is a system of homeostasis, but not due to the global size and a vast buffer capacity, but because of the high rate of reactions and presence of a program (genome) that allowed its development (ontogeny) independent from the outside environment. The early stages of the origin and evolution of the biosphere (from the RNA-world to the development of the prokaryotic ecosystems) were characterized by the domination of chemotrophic ecosystems. The geographical ranges of these ecosystems were directly or indirectly (through the atmosphere and hydrosphere) tied to the sources of nutrients in the geosphere, which were in turn connected to various sources of volcanic and geotectonic activity (geothermal waters, “black smokers” along the rift zones, etc.). This gave the biosphere consisting of chemotrophic ecosystems a mosaic appearance composed of separate local oases of life. The decrease of methane and accumulation of O₂ in the atmosphere in the geological evolution of the Earth caused the extinction of chemotrophic ecosystems and directed evolution of the biosphere toward autotrophy. Autotrophic photosynthesis gave the biosphere an energy source that was not connected to the geosphere, and for the first time allowed its liberation from the geosphere by developing its own vector of evolution. This vector resulted in the biosphere forming a continuous film of life on the planet by capturing the continents and occupying pelagic and abyssal zones, and the appearance of eukaryotes. The geosphere formed biogeochemical cycles in parallel to the geochemical ones, and comparable in the annual balances of participating matter.     

Evolutionary timing of the origins of mesophilic sulphate reduction and oxygenic photosynthesis: a phylogenomic dating approach

Until recently, the deep‐branching relationships in the bacterial domain have been unresolved. A new phylogenetic approach (termed compartmentalization) was able to resolve these deep‐branching relationships successfully by using a large number of genes from whole genome sequences and by reducing long branch attraction artefacts. This new, well‐resolved phylogenetic tree reveals the evolutionary relationships between diverse bacterial groups that leave important traces in the geological record. It shows that mesophilic sulphate reducers originated before the Cyanobacteria, followed by the origination of sulphur‐ and pyrite‐oxidizing bacteria after oxygen became available in the biosphere. This evolutionary pattern mirrors a similar pattern in the Palaeoproterozoic geological record. Sulphur isotopic fractionation records indicate that large‐scale bacterial sulphate reduction began in marine environments around 2.45 billion years ago (Ga), followed by rapid oxygenation of the atmosphere about 2.3 or 2.2 Ga. Oxygenation was then followed by increasing oceanic sulphate concentrations (probably owing to pyrite oxidation and continental weathering), which then resulted in the disappearance of banded iron formations by 1.8 Ga. The similarity between the phylogenetic and geological records suggests that the geochemical changes observed on the Palaeoproterozoic Earth were caused by major origination events in the mesophilic bacteria, and that these geochemical changes then caused additional origination events, such as aerobic respiration. If so, then constraints on divergence dates can be established for many microbial groups, including the Cyanobacteria, mesophilic bacteria, mesophilic sulphate reducers, methanotrophs, several anoxygenic phototrophs, as well as for mitochondrial endosymbiosis. These dates may also help to explain a large number of other changes in the geological record of the Neoarchean and Palaeoproterozoic Earth. This hypothesis, however, does not agree with the finding of cyanobacterial and eukaryote lipids at 2.7 Ga, and suggests that further work needs to be done to elucidate the discrepancies in both these areas.     

Atmospheric composition and climate on the early Earth

Oxygen isotope data from ancient sedimentary rocks appear to suggest that the early Earth was significantly warmer than today, with estimates of surface temperatures between 45 and 85 degrees C. We argue, following others, that this interpretation is incorrect-the same data can be explained via a change in isotopic composition of seawater with time. These changes in the isotopic composition could result from an increase in mean depth of the mid-ocean ridges caused by a decrease in geothermal heat flow with time. All this implies that the early Earth was warm, not hot.A more temperate early Earth is also easier to reconcile with the long-term glacial record. However, what triggered these early glaciations is still under debate. The Paleoproterozoic glaciations at approximately 2.4Ga were probably caused by the rise of atmospheric O2 and a concomitant decrease in greenhouse warming by CH4. Glaciation might have occurred in the Mid-Archaean as well, at approximately 2.9Ga, perhaps as a consequence of anti-greenhouse cooling by hydrocarbon haze. Both glaciations are linked to decreases in the magnitude of mass-independent sulphur isotope fractionation in ancient rocks. Studying both the oxygen and sulphur isotopic records has thus proved useful in probing the composition of the early atmosphere.     

Event energy clustering and evaluation based on shock wave model

Frequent occurrence of various events has a tremendous impact on daily social life; and how to accurately evaluate the generated energy by an event is the spot in the event study. With the rapid development of the internet technology, the internet web has become a good platform for evaluating event’s energy. Based on the physical shock wave model was firstly introduced to evaluate the generated energy by an event in this paper, this paper proposed a new method that the shock wave model was used to cluster classify with track sequential information under an action of an event. The experimental results show that it has a good consistency between the generated energy by an event under the shock wave model and people’s behavior affected by an event, and the proposed energy evaluation method is correct and practical.     

The science of the biosphere

This paper considers the needs and potentials for the development of the biosphere. An emphasis is placed on the unusual qualities of the biosphere, such as important time lags, interactions between life and its environment at large scales, and biological evolution, which has led to large scale changes in the environment during the Earth's history. These qualities require a different approach to the development of a theory for this large scale system than has been used in the past, when the biosphere was treated as a steady-state, quasilinear system. Other aspects of the development of the science of the biosphere, including the use of remote sensing, are reviewed, and the application of these techniques to the estimation of certain biological variables is discussed.     

When did oxygenic photosynthesis evolve?

The atmosphere has apparently been oxygenated since the 'Great Oxidation Event' ca 2.4 Ga ago, but when the photosynthetic oxygen production began is debatable. However, geological and geochemical evidence from older sedimentary rocks indicates that oxygenic photosynthesis evolved well before this oxygenation event. Fluid-inclusion oils in ca 2.45 Ga sandstones contain hydrocarbon biomarkers evidently sourced from similarly ancient kerogen, preserved without subsequent contamination, and derived from organisms producing and requiring molecular oxygen. Mo and Re abundances and sulphur isotope systematics of slightly older (2.5 Ga) kerogenous shales record a transient pulse of atmospheric oxygen. As early as ca 2.7 Ga, stromatolites and biomarkers from evaporative lake sediments deficient in exogenous reducing power strongly imply that oxygen-producing cyanobacteria had already evolved. Even at ca 3.2 Ga, thick and widespread kerogenous shales are consistent with aerobic photoautrophic marine plankton, and U-Pb data from ca 3.8 Ga metasediments suggest that this metabolism could have arisen by the start of the geological record. Hence, the hypothesis that oxygenic photosynthesis evolved well before the atmosphere became permanently oxygenated seems well supported.     

Giant deer: Origin, evolution, role in the biosphere

This monograph is devoted to the study of the giant deer or megacerines (tribe Megacerini, family Cervidae, order Artiodactyla) of the Late Cenozoic of Eurasia. Special attention is paid to megacerines of Inner Asia. This region, which is connected with the origin and early stages of historical development of megacerines, is key to gaining an insight into their evolution and phylogeny, place in the food chain, and effect on the biogeocoenoses. Based on the revision of fossil materials from the Upper Miocene-Lower Pleistocene of Russia, Mongolia, and Tajikistan, new data from Tuva, and analysis of an evolution, phylogeny, ecogenesis, diversity dynamics, stages of historical development, and place of megacerines in biogeocoenoses, their role in the maintenance of homeostasis of the biosphere and changes in environments are shown and certain basic principles of macroevolution and evolution of the biosphere are discussed.     

Effect of 3'-deoxyadenosine (cordycepin) on the early development of the sand dollar, Dendraster excentricus

The embryos of the sand dollar Dendraster excentricus have been examined with regard to their ability to undergo the early events of larval development in the presence of cordycepin, a reported inhibitor of RNA adenylylation. It has been shown that all the morphogenetic events from hatching to prism are inhibited by cordycepin at a concentration of 25 μg/ml, while the aspects of development prior to hatching (cleavage, blastulation, and the formation of cilia) are not affected by cordycepin. The period of sensitivity of each developmental event to cordycepin has been determined; for the early developmental processes this period substantially precedes the event, while for later processes there is a closer temporal association. In embryos treated with cordycepin, DNA synthesis and cleavage are unaffected prior to hatching, but subsequently are blocked, whereas respiration and total RNA synthesis per cell remain unaffected.     

Evolution of oxygenic photosynthesis: genome-wide analysis of the OEC extrinsic proteins

The appearance of oxygenic photosynthesis was a key event in the evolution of our green biosphere. Oxygen in the atmosphere is generally believed to come from the biomolecular water-splitting reaction that occurs in oxyphotosynthetic organisms catalysed by the oxygen evolving centre (OEC) of Photosystem II. Using knowledge from complete genomes and current databases, we have investigated the nature and composition of the extrinsic proteins forming the OECs of different organisms, with particular focus on the manganese stabilizing protein that is present in all known oxyphototrophs. This analysis traces the evolution of the extrinsic proteins from ancient cyanobacteria to higher plants and gives hints about the ancestral form of the OEC.     

Crown group Oxyphotobacteria postdate the rise of oxygen

The rise of oxygen ca. 2.3 billion years ago (Ga) is the most distinct environmental transition in Earth history. This event was enabled by the evolution of oxygenic photosynthesis in the ancestors of Cyanobacteria. However, long‐standing questions concern the evolutionary timing of this metabolism, with conflicting answers spanning more than one billion years. Recently, knowledge of the Cyanobacteria phylum has expanded with the discovery of non‐photosynthetic members, including a closely related sister group termed Melainabacteria, with the known oxygenic phototrophs restricted to a clade recently designated Oxyphotobacteria. By integrating genomic data from the Melainabacteria, cross‐calibrated Bayesian relaxed molecular clock analyses show that crown group Oxyphotobacteria evolved ca. 2.0 billion years ago (Ga), well after the rise of atmospheric dioxygen. We further estimate the divergence between Oxyphotobacteria and Melainabacteria ca. 2.5–2.6 Ga, which—if oxygenic photosynthesis is an evolutionary synapomorphy of the Oxyphotobacteria—marks an upper limit for the origin of oxygenic photosynthesis. Together, these results are consistent with the hypothesis that oxygenic photosynthesis evolved relatively close in time to the rise of oxygen.     

A hydrophobic cluster forms early in the folding of dihydrofolate reductase

The rapid kinetic phase that leads from unfolded species to transient folding intermediates in dihydrofolate reductase from Escherichia coli was examined by site-directed mutagenesis and by physicochemical means. The absence of this fluorescence-detected phase in the refolding of the Trp-74Phe mutant protein strongly implies that this early phase in refolding can be assigned to just one of the five Trp residues in the protein, Trp-74. In addition, water-soluble fluorescence quenching agents, iodide and cesium, have a much less significant effect on this early step in refolding than on the slower phases that lead to native and native-like conformers. These and other data imply that an important early event in the folding of dihydrofolate reductase is the formation of a hydrophobic cluster which protects Trp-74 from solvent.     

Thinking at the global scale

The noosphere concept was originally proposed as a sphere of mind or thought that has emerged from the biosphere over the course of human evolution. Two versions of the noosphere concept were developed in the 20th century and they differed with respect to whether the noosphere was to be considered separate from the biosphere or a new form of the biosphere. Both versions shared an assumption that collective human thought based on a scientific epistemology would achieve a benevolent relationship with the biosphere. Research in global ecology continues to reveal the growing influence of humanity on the biota and on the global biogeochemical cycles, but recent history has not confirmed humanity's ability to self‐regulate. Nevertheless, the noosphere concept remains useful because it acknowledges the uniquely subjective aspect of human brain functioning and the propensity for humans to share ideas and work collaboratively. Both of these features will be needed to develop a structured coupling of humanity and the biosphere that preserves the biophysical processes sustaining the ecosphere.     

The age of Rubisco: the evolution of oxygenic photosynthesis

The evolutionary history of oxygenesis is controversial. Form I of ribulose 1,5‐bisphosphate carboxylase/oxygenase (Rubisco) in oxygen‐tolerant organisms both enables them to carry out oxygenic extraction of carbon from air and enables the competitive process of photorespiration. Carbon isotopic evidence is presented from ~2.9 Ga stromatolites from Steep Rock, Ontario, Canada, ~2.9 Ga stromatolites from Mushandike, Zimbabwe, and ~2.7 Ga stromatolites in the Belingwe belt, Zimbabwe. The data imply that in all three localities the reef‐building autotrophs included organisms using Form I Rubisco. This inference, though not conclusive, is supported by other geochemical evidence that these stromatolites formed in oxic conditions. Collectively, the implication is that oxygenic photosynthesizers first appeared ~2.9 Ga ago, and were abundant 2.7–2.65 Ga ago. Rubisco specificity (its preference for CO₂ over O₂) and compensation constraints (the limits on carbon fixation) may explain the paradox that despite the inferred evolution of oxygenesis 2.9 Ga ago, the Late Archaean air was anoxic. The atmospheric CO₂:O₂ ratio, and hence greenhouse warming, may reflect Form I Rubisco's specificity for CO₂ over O₂. The system may be bistable under the warming Sun, with liquid oceans occurring in either anoxic (H₂O with abundant CH₄ plus CO₂) or oxic (H₂O with more abundant CO₂, but little CH₄) greenhouse states. Transition between the two states would involve catastrophic remaking of the biosphere. Build‐up of a very high atmospheric inventory of CO₂ in the 2.3 Ga glaciation may have allowed the atmosphere to move up the CO₂ compensation line to reach stability in an oxygen‐rich system. Since then, Form I Rubisco specificity and consequent compensation limits may have maintained the long‐term atmospheric disproportion between O₂ and CO₂, which is now close to both CO₂ and O₂ compensation barriers.     

Exchange of iron by gallium in siderophores

Siderophores are iron transport compounds produced by numerous microorganisms and which strongly chelate Fe(III), but not Fe(II). Other trivalent metals, such as Al(III), Cr(III), or Ga(III), are not capable of significantly displacing iron from siderophores. However, I demonstrate here that Ga(III) can effectively displace iron under reducing conditions. With ascorbate as reductant and ferrozine as Fe(II) trapping agent, the kinetics of reductive displacement of iron by Ga(III) were followed spectroscopically by the increase of absorbance at 562 nm due to formation of the Fe(II)-ferrozine complex. No significant reduction of siderophore occurred in the absence of Ga(III). With excess Ga(III), the displacement was quantitative and very rapid. The rate of metal exchange was pseudo first order with respect to Ga(III) concentration and highly pH dependent, suggesting that siderophore ligands are displaced from the iron in a concerted mechanism by Ga(III) and protonation to expose the Fe(III) to reduction by ascorbate. Reaction rates were dependent upon the structure of the siderophore, being greatest for ferric rhodotorulic acid and slowest for ferrichrome A at pH 5.4. The pH profile for ferric rhodotorulic acid was unusual in that it showed a maximum at pH 6.5, while all other siderophores examined showed an increase in rate as pH was lowered from 7.0. The physiological significance of this reaction to the clinical use of gallium is discussed.