Availability of O(2) and H(2)O(2) on pre-photosynthetic Earth

Was hydrogen peroxide present before the arrival of oxygenic photosynthesis? The important role of iron(II) in the Archean ocean

We address the chemical/biological history of H2O2 back at the times of the Archean eon (2.5-3.9 billion years ago (Gya)). During the Archean eon the pO2 was million-fold lower than the present pO2, starting to increase gradually from 2.3 until 0.6 Gya, when it reached ca. 0.2 bar. The observation that some anaerobic organisms can defend themselves against O2 has led to the view that early organisms could do the same before oxygenic photosynthesis had developed at about 3 Gya. This would require the anaerobic generation of H2O2, and here we examine the various mechanisms which were suggested in the literature for this. Given the concentration of Fe2+ at 20-200 μM in the Archean ocean, the estimated half-life of H2O2 is ca. 0.7 s. The oceanic H2O2 concentration was practically zero. We conclude that early organisms were not exposed to H2O2 before the arrival of oxygenic photosynthesis.

Photodissociation of CO2 via the 1Πg state: Wavelength-dependent imaging studies of O(1D2) photoproducts

Photodissociation of CO2 via the 1Πg state is investigated using a time-sliced velocity-mapped ion imaging apparatus combined with a tunable vacuum ultraviolet photolysis source. The main O(1D2) + CO(X1Σ+) channel is directly observed from the measured images of O(1D2) photoproducts at 129.08-134.76 nm. The total kinetic energy release spectra determined based on these images show that the energetic thresholds for the O(1D2) + CO(X1Σ+) photoproducts correspond to the thermochemical thresholds for the photodissociation of CO2(v2 = 0) and CO2(v2 = 1). One significant difference among the CO(X1Σ+, v) vibrational distributions for the predominant CO2(v2 = 0) dissociation is that the population of CO(v = 0) becomes favorable at 130.23-133.45 nm compared to the Boltzmann-like component (v > 0) that always exists at 129.08-134.76 nm. The wavelength dependences of the overall β are found to follow the variation trend of the CO(v = 0) abnormal intensity. The vibrational state-specific β values present a roughly decreasing trend with an increase in v, whereas β(v = 0) appears to be significantly larger than β(v = 1) at 130.23-133.45 nm compared to 134.76 and 129.08 nm. The non-statistical CO(v = 0) with larger β values at 130.23-133.45 nm implies that an additional pathway may open through the conical intersection coupling to the dissociative 21A'  state, except for the ever-existing pathway that yields the Boltzmann-like component. In contrast, at 129.08 nm, the restoration of the statistical equilibrium in the CO(X1Σ+, v) vibrational distribution may be caused by the emergence of novel dissociation pathways arising from the participation of the 31A″ state.

Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping

The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.

Vacuum ultraviolet photodissociation of sulfur dioxide and its implications for oxygen production in the early Earth's atmosphere

The emergence of molecular oxygen (O2) in the Earth's primitive atmosphere is an issue of major interest. Although the biological processes leading to its accumulation in the Earth's atmosphere are well understood, its abiotic source is still not fully established. Here, we report a new direct dissociation channel yielding S(1D) + O2(a1Δg/X3Σg-) products from vacuum ultraviolet (VUV) photodissociation of SO2 in the wavelength range between 120 and 160 nm. Experimental results show O2 production to be an important channel from SO2 VUV photodissociation, with a branching ratio of 30 ± 5% at the H Lyman-α wavelength (121.6 nm). The relatively large amounts of SO2 emitted from volcanic eruptions in the Earth's late Archaean eon imply that VUV photodissociation of SO2 could have provided a crucial additional source term in the O2 budget in the Earth's primitive atmosphere. The results could also have implications for abiotic oxygen formation on other planets with atmospheres rich in volcanically outgassed SO2.

Contact between water vapor and silicate surface causes abiotic formation of reactive oxygen species in an anoxic atmosphere

Spontaneous generation of reactive oxygen species (ROS) in aqueous microdroplets or at a water vapor-silicate interface is a new source of redox chemistry. However, such generation occurs with difficulty in liquid water having a large ionic strength. We report that ROS is spontaneously produced when water vapor contacts hydrogen-bonded hydroxyl groups on a silicate surface. The evolution of hydrogen-bonded species such as hydroxyl groups was investigated by using two-dimensional, time-resolved FT-IR spectroscopy. The participation of water vapor in ROS generation is confirmed by investigating the reaction of D2O vapor and hydroxyl groups on a silicate surface. We propose a reaction pathway for ROS generation based on the change of the hydrogen-bonding network and corresponding electron transfer onto the silicate surface in the water vapor-solid contact process. Our observations suggest that ROS production from water vapor-silicate contact electrification could have contributed to oxidation during the Archean Eon before the Great Oxidation Event.

Photodissociation study of CO2 on the formation of state-correlated CO(X1Σ+, v) with O(3P2) photoproducts in the low energy band centered at 148 nm

The spin-forbidden O(³P₂) + CO(X¹Σ⁺, v) channel formed from the photodissociation of CO₂ in the low energy band centered at 148 nm is investigated by using the time-sliced velocity-mapped ion imaging technique. The vibrational-resolved images of the O(³P₂) photoproducts measured in the photolysis wavelength range of 144.62-150.45 nm are analyzed to give the total kinetic energy releases (TKER) spectra, CO(X¹Σ⁺) vibrational state distributions, and anisotropy parameters (β). The TKER spectra reveal the formation of correlated CO(X¹Σ⁺) with well resolved v = 0-10 (or 11) vibrational bands. Several high vibrational bands that were observed in the low TKER region for each studied photolysis wavelength exhibit a bimodal structure. The CO(X¹Σ⁺, v) vibrational distributions all present inverted characteristics, and the most populated vibrational state changes from a low vibrational state to a relatively higher vibrational state with a change in the photolysis wavelength from 150.45 to 144.62 nm. However, the vibrational-state specific β-values for different photolysis wavelengths present a similar variation trend. The measured β-values show a significant bulge at the higher vibrational levels, in addition to the overall slow decreasing trend. The observed bimodal structures with mutational β-values for the high vibrational excited state CO(¹Σ⁺) photoproducts suggest the existence of more than one nonadiabatic pathway with different anisotropies in the formation of O(³P₂) + CO(X¹Σ⁺, v) photoproducts across the low energy band.

Natural Radioactivity and Chemical Evolution on the Early Earth: Prebiotic Chemistry and Oxygenation

It is generally recognized that the evolution of the early Earth was affected by an external energy source: radiation from the early Sun. The hypothesis about the important role of natural radioactivity, as a source of internal energy in the evolution of the early Earth, is considered and substantiated in this work. The decay of the long-lived isotopes ²³²Th, ²³⁸U, ²³⁵U, and ⁴⁰K in the Global Ocean initiated the oxygenation of the hydro- and atmosphere, and the abiogenesis. The content of isotopes in the ocean and the kinetics of their decay, the values of the absorbed dose and dose rate, and the efficiency of sea water radiolysis, as a function of time, were calculated. The ocean served as both a "reservoir" that collected components of the early atmosphere and products of their transformations, and a "converter" in which further chemical reactions of these compounds took place. Radical mechanisms were proposed for the formation of simple amino acids, sugars, and nitrogen bases, i.e., the key structures of all living things, and also for the formation of oxygen. The calculation results confirm the possible important role of natural radioactivity in the evolution of terrestrial matter, and the emergence of life.

Tectonically-driven oxidant production in the hot biosphere

Genomic reconstructions of the common ancestor to all life have identified genes involved in H₂O₂ and O₂ cycling. Commonly dismissed as an artefact of lateral gene transfer after oxygenic photosynthesis evolved, an alternative is a geological source of H₂O₂ and O₂ on the early Earth. Here, we show that under oxygen-free conditions high concentrations of H₂O₂ can be released from defects on crushed silicate rocks when water is added and heated to temperatures close to boiling point, but little is released at temperatures <80 °C. This temperature window overlaps the growth ranges of evolutionary ancient heat-loving and oxygen-respiring Bacteria and Archaea near the root of the Universal Tree of Life. We propose that the thermal activation of mineral surface defects during geological fault movements and associated stresses in the Earth’s crust was a source of oxidants that helped drive the (bio)geochemistry of hot fractures where life first evolved.

Researchers at Newcastle University have discovered a mechanism by which earthquakes create bursts of hydrogen peroxide and oxygen in hot underground fractures. These may have played a vital role in the early evolution and origin of life on Earth.

Chemical, Thermal, and Radiation Resistance of an Iron Porphyrin: A Model Study of Biosignature Stability

Metal complexes of porphyrins and porphyrin-type compounds are ubiquitous in all three domains of life, with hemes and chlorophylls being the best-known examples. Their diagenetic transformation products are found as geoporphyrins, in which the characteristic porphyrin core structure is retained and which can be up to 1.1 billion years old. Because of this, and their relative ease of detection, metalloporphyrins appear attractive as chemical biosignatures in the search for extraterrestrial life. In this study, we investigated the stability of solid chlorido(2,3,7,8,12,13,17,18-octaethylporphyrinato)iron(III) [FeCl(oep)], which served as a model for heme-like molecules and iron geoporphyrins. [FeCl(oep)] was exposed to a variety of astrobiologically relevant extreme conditions, namely: aqueous acids and bases, oxidants, heat, and radiation. Key results are: (1) the [Fe(oep)]⁺ core is stable over the pH range 0.0-13.5 even at 80°C; (2) the oxidizing power follows the order ClO^- > H₂O₂ > ClO₃^- > HNO₃ > ClO₄^-; (3) in an inert atmosphere, the iron porphyrin is thermally stable to near 250°C; (4) at high temperatures, carbon dioxide gas is not inert but acts as an oxidant, forming carbon monoxide; (5) a decomposition layer is formed on ultraviolet irradiation and protects the [FeCl(oep)] underneath; (6) an NaCl/NaHCO₃ salt mixture has a protective effect against X-rays; and (7) no such effect is observed when [FeCl(oep)] is exposed to iron ion particle radiation. The relevance to potential iron porphyrin biosignatures on Mars, Europa, and Enceladus is discussed.

The History of Ocean Oxygenation

The large-scale dynamics of ocean oxygenation have changed dramatically throughout Earth's history, in step with major changes in the abundance of O₂ in the atmosphere and changes to marine nutrient availability. A comprehensive mechanistic understanding of this history requires insights from oceanography, marine geology, geochemistry, geomicrobiology, evolutionary ecology, and Earth system modeling. Here, we attempt to synthesize the major features of evolving ocean oxygenation on Earth through more than 3 billion years of planetary history. We review the fundamental first-order controls on ocean oxygen distribution and summarize the current understanding of the history of ocean oxygenation on Earth from empirical and theoretical perspectives-integrating geochemical reconstructions of oceanic and atmospheric chemistry, genomic constraints on evolving microbial metabolism, and mechanistic biogeochemical models. These changes are used to illustrate primary regimes of large-scale ocean oxygenation and to highlight feedbacks that can act to stabilize and destabilize the ocean-atmosphere system in anoxic, low-oxygen, and high-oxygen states.

An abiotic source of Archean hydrogen peroxide and oxygen that pre-dates oxygenic photosynthesis

The evolution of oxygenic photosynthesis is a pivotal event in Earth's history because the O2 released fundamentally changed the planet's redox state and facilitated the emergence of multicellular life. An intriguing hypothesis proposes that hydrogen peroxide (H2O2) once acted as the electron donor prior to the evolution of oxygenic photosynthesis, but its abundance during the Archean would have been limited. Here, we report a previously unrecognized abiotic pathway for Archean H2O2 production that involves the abrasion of quartz surfaces and the subsequent generation of surface-bound radicals that can efficiently oxidize H2O to H2O2 and O2. We propose that in turbulent subaqueous environments, such as rivers, estuaries and deltas, this process could have provided a sufficient H2O2 source that led to the generation of biogenic O2, creating an evolutionary impetus for the origin of oxygenic photosynthesis.

Microbial helpers allow cyanobacteria to thrive in ferruginous waters

The Great Oxidation Event (GOE) was a rapid accumulation of oxygen in the atmosphere as a result of the photosynthetic activity of cyanobacteria. This accumulation reflected the pervasiveness of O₂ on the planet's surface, indicating that cyanobacteria had become ecologically successful in Archean oceans. Micromolar concentrations of Fe²⁺ in Archean oceans would have reacted with hydrogen peroxide, a byproduct of oxygenic photosynthesis, to produce hydroxyl radicals, which cause cellular damage. Yet, cyanobacteria colonized Archean oceans extensively enough to oxygenate the atmosphere, which likely required protection mechanisms against the negative impacts of hydroxyl radical production in Fe²⁺ -rich seas. We identify several factors that could have acted to protect early cyanobacteria from the impacts of hydroxyl radical production and hypothesize that microbial cooperation may have played an important role in protecting cyanobacteria from Fe²⁺ toxicity before the GOE. We found that several strains of facultative anaerobic heterotrophic bacteria (Shewanella) with ROS defence mechanisms increase the fitness of cyanobacteria (Synechococcus) in ferruginous waters. Shewanella species with manganese transporters provided the most protection. Our results suggest that a tightly regulated response to prevent Fe²⁺ toxicity could have been important for the colonization of ancient ferruginous oceans, particularly in the presence of high manganese concentrations and may expand the upper bound for tolerable Fe²⁺ concentrations for cyanobacteria.

Fast Degradation of Hydrogen Peroxide by Immobilized Catalase to Enable the Use of Biosensors in Extraterrestrial Bodies

Hydrogen peroxide has been postulated to be present on the surface of Europa and Enceladus. While it could represent a potential source of energy for possible life-forms, H₂O₂ may also interfere with a number of current detection technologies, including biosensors. To take advantage of the selectivity and portability of these devices, simple and reliable routes to degrade the potential H₂O₂ present should be developed and implemented to prepare for this possibility. Unfortunately, most of the current approaches for removing H₂O₂ are slow, may affect the sample, or could interfere with the performance of biosensors. To address these limitations, catalase was immobilized onto silica particles and used as a means to selectively decompose H₂O₂ prior to the analysis of common biomarkers with a biosensor. For these experiments, glucose, l-leucine, and lactic acid were used as representative examples of biomolecules such as carbohydrates, amino acids, and organic acids, respectively, which could be used as biomarkers on extraterrestrial bodies. While the decomposition reaction between catalase and H₂O₂ is well known, to our knowledge this is the first instance where catalase has been used in combination with a microfluidic paper-based analytical device (μPAD) to implement selective sample pretreatment.

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.

How to define obligatory anaerobiosis? An evolutionary view on the antioxidant response system and the early stages of the evolution of life on Earth

One of the former definitions of "obligate anaerobiosis" was based on three main criteria: 1) it occurs in organisms, so-called obligate anaerobes, which live in environments without oxygen (O₂), 2) O₂-dependent (aerobic) respiration, and 3) antioxidant enzymes are absent in obligate anaerobes. In contrast, aerobes need O₂ in order to grow and develop properly. Obligate (or strict) anaerobes belong to prokaryotic microorganisms from two domains, Bacteria and Archaea. A closer look at anaerobiosis covers a wide range of microorganisms that permanently or in a time-dependent manner tolerate different concentrations of O₂ in their habitats. On this basis they can be classified as obligate/facultative anaerobes, microaerophiles and nanaerobes. Paradoxically, O₂ tolerance in strict anaerobes is usually, as in aerobes, associated with the activity of the antioxidant response system, which involves different antioxidant enzymes responsible for removing excess reactive oxygen species (ROS). In our opinion, the traditional definition of "obligate anaerobiosis" loses its original sense. Strict anaerobiosis should only be restricted to the occurrence of O₂-independent pathways involved in energy generation. For that reason, a term better than "obligate anaerobes" would be O₂/ROS tolerant anaerobes, where the role of the O₂/ROS detoxification system is separated from O₂-independent metabolic pathways that supply energy. Ubiquitous key antioxidant enzymes like superoxide dismutase (SOD) and superoxide reductase (SOR) in contemporary obligate anaerobes might suggest that their origin is ancient, maybe even the beginning of the evolution of life on Earth. It cannot be ruled out that c. 3.5 Gyr ago, local microquantities of O₂/ROS played a role in the evolution of the last universal common ancestor (LUCA) of all modern organisms. On the basis of data in the literature, the hypothesis that LUCA could be an O₂/ROS tolerant anaerobe is discussed together with the question of the abiotic sources of O₂/ROS and/or the early evolution of cyanobacteria that perform oxygenic photosynthesis.

An investigation into the effects of increasing salinity on photosynthesis in freshwater unicellular cyanobacteria during the late Archaean

The oldest species of bacteria capable of oxygenic photosynthesis today are the freshwater Cyanobacteria Gloeobacter spp., belonging to the class Oxyphotobacteria. Several modern molecular evolutionary studies support the freshwater origin of cyanobacteria during the Archaean and their subsequent acquisition of salt tolerance mechanisms necessary for their expansion into the marine environment. This study investigated the effect of a sudden washout event from a freshwater location into either a brackish or marine environment on the photosynthetic efficiency of two unicellular freshwater cyanobacteria: the salt-tolerant Chroococcidiopsis thermalis PCC7203 and the cyanobacterial phylogenetic root species, Gloeobacter violaceus PCC7421. Strains were cultured under present atmospheric levels (PAL) of CO₂ or an atmosphere containing elevated levels of CO₂ and reduced O₂ (eCO₂ rO₂ ) in simulated shallow water or terrestrial environmental conditions. Both strains exhibited a reduction in growth rates and gross photosynthesis, accompanied by significant reductions in chlorophyll a content, in brackish water, with only C. thermalis able to grow at marine salinity levels. While the experimental atmosphere caused a significant increase in gross photosynthesis rates in both strains, it did not increase their growth rates, nor the amount of O₂ released. The differences in growth responses to increasing salinities could be attributed to genetic differences, with C. thermalis carrying additional genes for trehalose synthesis. This study demonstrates that, if cyanobacteria did evolve in a freshwater environment, they would have been capable of withstanding a sudden washout into increasingly saline environments. Both C. thermalis and G. violaceus continued to grow and photosynthesise, albeit at diminished rates, in brackish water, thereby providing a route for the evolution of open ocean-dwelling strains, necessary for the oxygenation of the Earth's atmosphere.

Reactive Oxygen Species: Radical Factors in the Evolution of Animal Life: A molecular timescale from Earth's earliest history to the rise of complex life

Introduction of O₂ to Earth's early biosphere stimulated remarkable evolutionary adaptations, and a wide range of electron acceptors allowed diverse, energy-yielding metabolic pathways. Enzymatic reduction of O₂ yielded a several-fold increase in energy production, enabling evolution of multi-cellular animal life. However, utilization of O₂ also presented major challenges as O₂ and many of its derived reactive oxygen species (ROS) are highly toxic, possibly impeding multicellular evolution after the Great Oxidation Event. Remarkably, ROS, and especially hydrogen peroxide, seem to play a major part in early diversification and further development of cellular respiration and other oxygenic pathways, thus becoming an intricate part of evolution of complex life. Hence, although harnessing of chemical and thermo-dynamic properties of O₂ for aerobic metabolism is generally considered to be an evolutionary milestone, the ability to use ROS for cell signaling and regulation may have been the first true breakthrough in development of complex life.

RubisCO Early Oxygenase Activity: A Kinetic and Evolutionary Perspective

RubisCO (D-ribulose 1,5-bisphosphate carboxylase/oxygenase) is Earth's main enzyme responsible for CO₂ fixation via carboxylation of ribulose-1,5-bisphosphate (RuBP) into organic matter. Besides the carboxylation reaction, RubisCO also catalyzes the oxygenation of RuBP by O₂ , which is probably as old as its carboxylation properties. Based on molecular phylogeny, the occurrence of the reactive oxygen species (ROS)-removing system and kinetic properties of different RubisCO forms, we postulated that RubisCO oxygenase activity appeared in local microoxic areas, yet before the appearance of oxygenic photosynthesis. Here, in reviewing the literature, we present a novel hypothesis: the RubisCO early oxygenase activity hypothesis. This hypothesis may be compared with the exaptation hypothesis, according to which latent RubisCO oxygenase properties emerged later during the oxygenation of the Earth's atmosphere. The reconstruction of ancestral RubisCO forms using ancestral sequence reconstruction (ASR) techniques, as a promising way for testing of RubisCO early oxygenase activity hypothesis, is presented.

Photoferrotrophy: Remains of an Ancient Photosynthesis in Modern Environments

Photoferrotrophy, the process by which inorganic carbon is fixed into organic matter using light as an energy source and reduced iron [Fe(II)] as an electron donor, has been proposed as one of the oldest photoautotrophic metabolisms on Earth. Under the iron-rich (ferruginous) but sulfide poor conditions dominating the Archean ocean, this type of metabolism could have accounted for most of the primary production in the photic zone. Here we review the current knowledge of biogeochemical, microbial and phylogenetic aspects of photoferrotrophy, and evaluate the ecological significance of this process in ancient and modern environments. From the ferruginous conditions that prevailed during most of the Archean, the ancient ocean evolved toward euxinic (anoxic and sulfide rich) conditions and, finally, much after the advent of oxygenic photosynthesis, to a predominantly oxic environment. Under these new conditions photoferrotrophs lost importance as primary producers, and now photoferrotrophy remains as a vestige of a formerly relevant photosynthetic process. Apart from the geological record and other biogeochemical markers, modern environments resembling the redox conditions of these ancient oceans can offer insights into the past significance of photoferrotrophy and help to explain how this metabolism operated as an important source of organic carbon for the early biosphere. Iron-rich meromictic (permanently stratified) lakes can be considered as modern analogs of the ancient Archean ocean, as they present anoxic ferruginous water columns where light can still be available at the chemocline, thus offering suitable niches for photoferrotrophs. A few bacterial strains of purple bacteria as well as of green sulfur bacteria have been shown to possess photoferrotrophic capacities, and hence, could thrive in these modern Archean ocean analogs. Studies addressing the occurrence and the biogeochemical significance of photoferrotrophy in ferruginous environments have been conducted so far in lakes Matano, Pavin, La Cruz, and the Kabuno Bay of Lake Kivu. To date, only in the latter two lakes a biogeochemical role of photoferrotrophs has been confirmed. In this review we critically summarize the current knowledge on iron-driven photosynthesis, as a remains of ancient Earth biogeochemistry.

Evolution of Earth-like Extrasolar Planetary Atmospheres: Assessing the Atmospheres and Biospheres of Early Earth Analog Planets with a Coupled Atmosphere Biogeochemical Model

Understanding the evolution of Earth and potentially habitable Earth-like worlds is essential to fathom our origin in the Universe. The search for Earth-like planets in the habitable zone and investigation of their atmospheres with climate and photochemical models is a central focus in exoplanetary science. Taking the evolution of Earth as a reference for Earth-like planets, a central scientific goal is to understand what the interactions were between atmosphere, geology, and biology on early Earth. The Great Oxidation Event in Earth's history was certainly caused by their interplay, but the origin and controlling processes of this occurrence are not well understood, the study of which will require interdisciplinary, coupled models. In this work, we present results from our newly developed Coupled Atmosphere Biogeochemistry model in which atmospheric O₂ concentrations are fixed to values inferred by geological evidence. Applying a unique tool (Pathway Analysis Program), ours is the first quantitative analysis of catalytic cycles that governed O₂ in early Earth's atmosphere near the Great Oxidation Event. Complicated oxidation pathways play a key role in destroying O₂, whereas in the upper atmosphere, most O₂ is formed abiotically via CO₂ photolysis. The O₂ bistability found by Goldblatt et al. ( 2006 ) is not observed in our calculations likely due to our detailed CH₄ oxidation scheme. We calculate increased CH₄ with increasing O₂ during the Great Oxidation Event. For a given atmospheric surface flux, different atmospheric states are possible; however, the net primary productivity of the biosphere that produces O₂ is unique. Mixing, CH₄ fluxes, ocean solubility, and mantle/crust properties strongly affect net primary productivity and surface O₂ fluxes. Regarding exoplanets, different "states" of O₂ could exist for similar biomass output. Strong geological activity could lead to false negatives for life (since our analysis suggests that reducing gases remove O₂ that masks its biosphere over a wide range of conditions). Key Words: Early Earth-Proterozoic-Archean-Oxygen-Atmosphere-Biogeochemistry-Photochemistry-Biosignatures-Earth-like planets. Astrobiology 16, 27-54.

Chromium geochemistry of the ca. 1.85 Ga Flin Flon paleosol

Fractionation of stable Cr isotopes has been measured in Archaean paleosols and marine sedimentary rocks and interpreted to record the terrestrial oxidation of Cr(III) to Cr(VI), providing possible indirect evidence for the emergence of oxygenic photosynthesis. However, these fractionations occur amidst evidence from other geochemical proxies for a pervasively anoxic atmosphere. This study examined the Cr geochemistry of the ca. 1.85 Ga Flin Flon paleosol, which developed under an atmosphere unambiguously oxidising enough to quantitatively convert Fe(II) to Fe(III) during pedogenesis. The paleosol shows an extreme range in Cr isotope composition of 2.76 ‰ δ^53/52 Cr. The protolith greenstone (δ^53/52 Cr: -0.23 ‰), the deepest weathering horizon (δ^53/52 Cr: -0.15 to -0.23 ‰) and a residual corestone in the upper paleosol (δ^53/52 Cr: -0.01 ‰) all exhibit Cr isotopic compositions comparable to unaltered igneous rocks. The most significant isotopic fractionation is preserved in the areas influenced by oxidative subaerial weathering (i.e. increase in Fe(III)/Fe(II)) and the greatest loss of mobile elements. The uppermost paleosol horizon is both Cr and Mn depleted and offset to significantly ⁵³ Cr-enriched compositions (δ^53/52 Cr values between +1.50 and +2.38 ‰), which is not easily modelled with the oxidation of Cr(III) and loss of isotopically heavy Cr(VI). Instead, the currently preferred model for these data invokes the open-system removal of isotopically light aqueous Cr(III) during either pedogenesis or subsequent hydrothermal/metamorphic alteration. The ⁵³ Cr enrichment would then represent the preferential dissolution or complexation of isotopically light aqueous Cr(III) species (enhanced by lower pH conditions and possibly the presence of complexing ligands) and/or the residual signature from preferential adsorption of isotopically heavy Cr(III). Both scenarios would contradict the widely held assumption that only redox reactions of Cr can generate large magnitude isotopic fractionations and, if substantiated, non-redox isotope effects would complicate the conclusive fingerprinting of ancient atmospheric O₂ from Cr isotope data alone.

Follow the Carbon: Isotopic Labeling Studies of Early Earth Aerosol

Despite the faint young Sun, early Earth might have been kept warm by an atmosphere containing the greenhouse gases CH₄ and CO₂ in mixing ratios higher than those found on Earth today. Laboratory and modeling studies suggest that an atmosphere containing these trace gases could lead to the formation of organic aerosol haze due to UV photochemistry. Chemical mechanisms proposed to explain haze formation rely on CH₄ as the source of carbon and treat CO₂ as a source of oxygen only, but this has not previously been verified experimentally. In the present work, we use isotopically labeled precursor gases and unit-mass resolution (UMR) and high-resolution (HR) aerosol mass spectrometry to examine the sources of carbon and oxygen to photochemical aerosol formed in a CH₄/CO₂/N₂ atmosphere. UMR results suggest that CH₄ contributes 70-100% of carbon in the aerosol, while HR results constrain the value from 94% to 100%. We also confirm that CO₂ contributes approximately 10% of the total mass to the aerosol as oxygen. These results have implications for the geochemical interpretations of inclusions found in Archean rocks on Earth and for the astrobiological potential of other planetary atmospheres. Key Words: Atmosphere-Early Earth-Planetary atmospheres-Carbon dioxide-Methane. Astrobiology 16, 822-830.

Enzymatic Antioxidant Systems in Early Anaerobes: Theoretical Considerations

It is widely accepted that cyanobacteria-dependent oxygen that was released into Earth's atmosphere ca. 2.5 billion years ago sparked the evolution of the aerobic metabolism and the antioxidant system. In modern aerobes, enzymes such as superoxide dismutases (SODs), peroxiredoxins (PXs), and catalases (CATs) constitute the core of the enzymatic antioxidant system (EAS) directed against reactive oxygen species (ROS). In many anaerobic prokaryotes, the superoxide reductases (SORs) have been identified as the main force in counteracting ROS toxicity. We found that 93% of the analyzed strict anaerobes possess at least one antioxidant enzyme, and 50% have a functional EAS, that is, consisting of at least two antioxidant enzymes: one for superoxide anion radical detoxification and another for hydrogen peroxide decomposition. The results presented here suggest that the last universal common ancestor (LUCA) was not a strict anaerobe. O2 could have been available for the first microorganisms before oxygenic photosynthesis evolved, however, from the intrinsic activity of EAS, not solely from abiotic sources.

KEY WORDS

Archaea-Atmospheric gases-Evolution-H2O2 resistance-Oxygenic photosynthesis. Astrobiology 16, 348-358.

Timescales of Oxygenation Following the Evolution of Oxygenic Photosynthesis

Among the most important bioenergetic innovations in the history of life was the invention of oxygenic photosynthesis-autotrophic growth by splitting water with sunlight-by Cyanobacteria. It is widely accepted that the invention of oxygenic photosynthesis ultimately resulted in the rise of oxygen by ca. 2.35 Gya, but it is debated whether this occurred more or less immediately as a proximal result of the evolution of oxygenic Cyanobacteria or whether they originated several hundred million to more than one billion years earlier in Earth history. The latter hypothesis involves a prolonged period during which oxygen production rates were insufficient to oxidize the atmosphere, potentially due to redox buffering by reduced species such as higher concentrations of ferrous iron in seawater. To examine the characteristic timescales for environmental oxygenation following the evolution of oxygenic photosynthesis, we applied a simple mathematical approach that captures many of the salient features of the major biogeochemical fluxes and reservoirs present in Archean and early Paleoproterozoic surface environments. Calculations illustrate that oxygenation would have overwhelmed redox buffers within ~100 kyr following the emergence of oxygenic photosynthesis, a geologically short amount of time unless rates of primary production were far lower than commonly expected. Fundamentally, this result arises because of the multiscale nature of the carbon and oxygen cycles: rates of gross primary production are orders of magnitude too fast for oxygen to be masked by Earth's geological buffers, and can only be effectively matched by respiration at non-negligible O2 concentrations. These results suggest that oxygenic photosynthesis arose shortly before the rise of oxygen, not hundreds of millions of years before it.

A PROPOSAL FOR CLIMATE STABILITY ON H2-GREENHOUSE PLANETS

A terrestrial planet in an orbit far outside of the standard habitable zone could maintain surface liquid water as a result of H₂-H₂ collision-induced absorption by a thick H₂ atmosphere. Without a stabilizing climate feedback, however, habitability would be accidental and likely brief. In this letter I propose stabilizing climate feedbacks for such a planet that require only that biological functions have an optimal temperature and operate less efficiently at other temperatures. For example, on a planet with a net source of H₂ from its interior, H₂-consuming life (such as methanogens) could establish a stable climate. If a positive perturbation is added to the equilibrium temperature, H₂ consumption by life will increase (cooling the planet) until the equilibrium climate is reestablished. The potential existence of such feedbacks makes H₂-warmed planets more attractive astrobiological targets.

The evolution of respiratory O2/NO reductases: an out-of-the-phylogenetic-box perspective

Complex life on our planet crucially depends on strong redox disequilibria afforded by the almost ubiquitous presence of highly oxidizing molecular oxygen. However, the history of O2-levels in the atmosphere is complex and prior to the Great Oxidation Event some 2.3 billion years ago, the amount of O2 in the biosphere is considered to have been extremely low as compared with present-day values. Therefore the evolutionary histories of life and of O2-levels are likely intricately intertwined. The obvious biological proxy for inferring the impact of changing O2-levels on life is the evolutionary history of the enzyme allowing organisms to tap into the redox power of molecular oxygen, i.e. the bioenergetic O2 reductases, alias the cytochrome and quinol oxidases. Consequently, molecular phylogenies reconstructed for this enzyme superfamily have been exploited over the last two decades in attempts to elucidate the interlocking between O2 levels in the environment and the evolution of respiratory bioenergetic processes. Although based on strictly identical datasets, these phylogenetic approaches have led to diametrically opposite scenarios with respect to the history of both the enzyme superfamily and molecular oxygen on the Earth. In an effort to overcome the deadlock of molecular phylogeny, we here review presently available structural, functional, palaeogeochemical and thermodynamic information pertinent to the evolution of the superfamily (which notably also encompasses the subfamily of nitric oxide reductases). The scenario which, in our eyes, most closely fits the ensemble of these non-phylogenetic data, sees the low O2-affinity SoxM- (or A-) type enzymes as the most recent evolutionary innovation and the high-affinity O2 reductases (SoxB or B and cbb3 or C) as arising independently from NO-reducing precursor enzymes.

Benthic perspective on Earth's oldest evidence for oxygenic photosynthesis

The Great Oxidation Event (GOE) is currently viewed as a protracted process during which atmospheric oxygen increased above ∼10(-5) times the present atmospheric level (PAL). This threshold represents an estimated upper limit for sulfur isotope mass-independent fractionation (S-MIF), an Archean signature of atmospheric anoxia that begins to disappear from the rock record at 2.45 Ga. However, an increasing number of papers have suggested that the timing for oxidative continental weathering, and by conventional thinking the onset of atmospheric oxygenation, was hundreds of million years earlier than previously thought despite the presence of S-MIF. We suggest that this apparent discrepancy can be resolved by the earliest oxidative-weathering reactions occurring in benthic and soil environments at profound redox disequilibrium with the atmosphere, such as biological soil crusts and freshwater microbial mats covering riverbed, lacustrine, and estuarine sediments. We calculate that oxygenic photosynthesis in these millimeter-thick ecosystems provides sufficient oxidizing equivalents to mobilize sulfate and redox-sensitive trace metals from land to the oceans while the atmosphere itself remained anoxic with its attendant S-MIF signature. As continental freeboard increased significantly between 3.0 and 2.5 Ga, the chemical and isotopic signatures of benthic oxidative weathering would have become more globally significant from a mass-balance perspective. These observations help reconcile evidence for pre-GOE oxidative weathering with the history of atmospheric chemistry, and support the plausible antiquity of a terrestrial biosphere populated by cyanobacteria well before the GOE.

Atmospheric hydrogen peroxide and Eoarchean iron formations

It is widely accepted that photosynthetic bacteria played a crucial role in Fe(II) oxidation and the precipitation of iron formations (IF) during the Late Archean-Early Paleoproterozoic (2.7-2.4 Ga). It is less clear whether microbes similarly caused the deposition of the oldest IF at ca. 3.8 Ga, which would imply photosynthesis having already evolved by that time. Abiological alternatives, such as the direct oxidation of dissolved Fe(II) by ultraviolet radiation may have occurred, but its importance has been discounted in environments where the injection of high concentrations of dissolved iron directly into the photic zone led to chemical precipitation reactions that overwhelmed photooxidation rates. However, an outstanding possibility remains with respect to photochemical reactions occurring in the atmosphere that might generate hydrogen peroxide (H2 O2 ), a recognized strong oxidant for ferrous iron. Here, we modeled the amount of H2 O2 that could be produced in an Eoarchean atmosphere using updated solar fluxes and plausible CO2 , O2 , and CH4 mixing ratios. Irrespective of the atmospheric simulations, the upper limit of H2 O2 rainout was calculated to be <10(6) molecules cm(-2) s(-1) . Using conservative Fe(III) sedimentation rates predicted for submarine hydrothermal settings in the Eoarchean, we demonstrate that the flux of H2 O2 was insufficient by several orders of magnitude to account for IF deposition (requiring ~10(11) H2 O2 molecules cm(-2) s(-1) ). This finding further constrains the plausible Fe(II) oxidation mechanisms in Eoarchean seawater, leaving, in our opinion, anoxygenic phototrophic Fe(II)-oxidizing micro-organisms the most likely mechanism responsible for Earth's oldest IF.

Communication: direct measurements of nascent O((3)P0,1,2) fine-structure distributions and branching ratios of correlated spin-orbit resolved product channels CO(ã(3)Π; v) + O((3)P0,1,2) and CO(X̃(1)Σ(+); v) + O((3)P0,1,2) in VUV photodissociation of CO2

We present a generally applicable experimental method for the direct measurement of nascent spin-orbit state distributions of atomic photofragments based on the detection of vacuum ultraviolet (VUV)-excited autoionizing-Rydberg (VUV-EAR) states. The incorporation of this VUV-EAR method in the application of the newly established VUV-VUV laser velocity-map-imaging-photoion (VMI-PI) apparatus has made possible the branching ratio measurement for correlated spin-orbit state resolved product channels, CO(ã(3)Π; v) + O((3)P0,1,2) and CO(X̃(1)Σ(+); v) + O((3)P0,1,2), formed by VUV photoexcitation of CO2 to the 4s(10 (1)) Rydberg state at 97,955.7 cm(-1). The total kinetic energy release (TKER) spectra obtained from the O(+) VMI-PI images of O((3)P0,1,2) reveal the formation of correlated CO(ã(3)Π; v = 0-2) with well-resolved v = 0-2 vibrational bands. This observation shows that the dissociation of CO2 to form the spin-allowed CO(ã(3)Π; v = 0-2) + O((3)P0,1,2) channel has no potential energy barrier. The TKER spectra for the spin-forbidden CO(X̃(1)Σ(+); v) + O((3)P0,1,2) channel were found to exhibit broad profiles, indicative of the formation of a broad range of rovibrational states of CO(X̃(1)Σ(+)) with significant vibrational populations for v = 18-26. While the VMI-PI images for the CO(ã(3)Π; v = 0-2) + O((3)P0,1,2) channel are anisotropic, indicating that the predissociation of CO2 4s(10 (1)) occurs via a near linear configuration in a time scale shorter than the rotational period, the angular distributions for the CO(X̃(1)Σ(+); v) + O((3)P0,1,2) channel are close to isotropic, revealing a slower predissociation process, which possibly occurs on a triplet surface via an intersystem crossing mechanism.

The energetics of organic synthesis inside and outside the cell

Thermodynamic modelling of organic synthesis has largely been focused on deep-sea hydrothermal systems. When seawater mixes with hydrothermal fluids, redox gradients are established that serve as potential energy sources for the formation of organic compounds and biomolecules from inorganic starting materials. This energetic drive, which varies substantially depending on the type of host rock, is present and available both for abiotic (outside the cell) and biotic (inside the cell) processes. Here, we review and interpret a library of theoretical studies that target organic synthesis energetics. The biogeochemical scenarios evaluated include those in present-day hydrothermal systems and in putative early Earth environments. It is consistently and repeatedly shown in these studies that the formation of relatively simple organic compounds and biomolecules can be energy-yielding (exergonic) at conditions that occur in hydrothermal systems. Expanding on our ability to calculate biomass synthesis energetics, we also present here a new approach for estimating the energetics of polymerization reactions, specifically those associated with polypeptide formation from the requisite amino acids.

Manganese-oxidizing photosynthesis before the rise of cyanobacteria

The emergence of oxygen-producing (oxygenic) photosynthesis fundamentally transformed our planet; however, the processes that led to the evolution of biological water splitting have remained largely unknown. To illuminate this history, we examined the behavior of the ancient Mn cycle using newly obtained scientific drill cores through an early Paleoproterozoic succession (2.415 Ga) preserved in South Africa. These strata contain substantial Mn enrichments (up to ∼17 wt %) well before those associated with the rise of oxygen such as the ∼2.2 Ga Kalahari Mn deposit. Using microscale X-ray spectroscopic techniques coupled to optical and electron microscopy and carbon isotope ratios, we demonstrate that the Mn is hosted exclusively in carbonate mineral phases derived from reduction of Mn oxides during diagenesis of primary sediments. Additional observations of independent proxies for O2--multiple S isotopes (measured by isotope-ratio mass spectrometry and secondary ion mass spectrometry) and redox-sensitive detrital grains--reveal that the original Mn-oxide phases were not produced by reactions with O2, which points to a different high-potential oxidant. These results show that the oxidative branch of the Mn cycle predates the rise of oxygen, and provide strong support for the hypothesis that the water-oxidizing complex of photosystem II evolved from a former transitional photosystem capable of single-electron oxidation reactions of Mn.

Oxygen and hydrogen peroxide in the early evolution of life on earth: in silico comparative analysis of biochemical pathways

In the Universe, oxygen is the third most widespread element, while on Earth it is the most abundant one. Moreover, oxygen is a major constituent of all biopolymers fundamental to living organisms. Besides O(2), reactive oxygen species (ROS), among them hydrogen peroxide (H(2)O(2)), are also important reactants in the present aerobic metabolism. According to a widely accepted hypothesis, aerobic metabolism and many other reactions/pathways involving O(2) appeared after the evolution of oxygenic photosynthesis. In this study, the hypothesis was formulated that the Last Universal Common Ancestor (LUCA) was at least able to tolerate O(2) and detoxify ROS in a primordial environment. A comparative analysis was carried out of a number of the O(2)-and H(2)O(2)-involving metabolic reactions that occur in strict anaerobes, facultative anaerobes, and aerobes. The results indicate that the most likely LUCA possessed O(2)-and H(2)O(2)-involving pathways, mainly reactions to remove ROS, and had, at least in part, the components of aerobic respiration. Based on this, the presence of a low, but significant, quantity of H(2)O(2) and O(2) should be taken into account in theoretical models of the early Archean atmosphere and oceans and the evolution of life. It is suggested that the early metabolism involving O(2)/H(2)O(2) was a key adaptation of LUCA to already existing weakly oxic zones in Earth's primordial environment.

Microaerobic steroid biosynthesis and the molecular fossil record of Archean life

The power of molecular oxygen to drive many crucial biogeochemical processes, from cellular respiration to rock weathering, makes reconstructing the history of its production and accumulation a first-order question for understanding Earth's evolution. Among the various geochemical proxies for the presence of O(2) in the environment, molecular fossils offer a unique record of O(2) where it was first produced and consumed by biology: in sunlit aquatic habitats. As steroid biosynthesis requires molecular oxygen, fossil steranes have been used to draw inferences about aerobiosis in the early Precambrian. However, better quantitative constraints on the O(2) requirement of this biochemistry would clarify the implications of these molecular fossils for environmental conditions at the time of their production. Here we demonstrate that steroid biosynthesis is a microaerobic process, enabled by dissolved O(2) concentrations in the nanomolar range. We present evidence that microaerobic marine environments (where steroid biosynthesis was possible) could have been widespread and persistent for long periods of time prior to the earliest geologic and isotopic evidence for atmospheric O(2). In the late Archean, molecular oxygen likely cycled as a biogenic trace gas, much as compounds such as dimethylsulfide do today.