The Archean atmosphere

Volatile Organic Compound Metabolism on Early Earth

Biogenic volatile organic compounds (VOCs) constitute a significant portion of gas-phase metabolites in modern ecosystems and have unique roles in moderating atmospheric oxidative capacity, solar radiation balance, and aerosol formation. It has been theorized that VOCs may account for observed geological and evolutionary phenomena during the Archaean, but the direct contribution of biology to early non-methane VOC cycling remains unexplored. Here, we provide an assessment of all potential VOCs metabolized by the last universal common ancestor (LUCA). We identify enzyme functions linked to LUCA orthologous protein groups across eight literature sources and estimate the volatility of all associated substrates to identify ancient volatile metabolites. We hone in on volatile metabolites with confirmed modern emissions that exist in conserved metabolic pathways and produce a curated list of the most likely LUCA VOCs. We introduce volatile organic metabolites associated with early life and discuss their potential influence on early carbon cycling and atmospheric chemistry.

Co-evolution of early Earth environments and microbial life

Two records of Earth history capture the evolution of life and its co-evolving ecosystems with interpretable fidelity: the geobiological and geochemical traces preserved in rocks and the evolutionary histories captured within genomes. The earliest vestiges of life are recognized mostly in isotopic fingerprints of specific microbial metabolisms, whereas fossils and organic biomarkers become important later. Molecular biology provides lineages that can be overlayed on geologic and geochemical records of evolving life. All these data lie within a framework of biospheric evolution that is primarily characterized by the transition from an oxygen-poor to an oxygen-rich world. In this Review, we explore the history of microbial life on Earth and the degree to which it shaped, and was shaped by, fundamental transitions in the chemical properties of the oceans, continents and atmosphere. We examine the diversity and evolution of early metabolic processes, their couplings with biogeochemical cycles and their links to the oxygenation of the early biosphere. We discuss the distinction between the beginnings of metabolisms and their subsequent proliferation and their capacity to shape surface environments on a planetary scale. The evolution of microbial life and its ecological impacts directly mirror the Earth's chemical and physical evolution through cause-and-effect relationships.

Self-Oxidation of the Atmospheres of Rocky Planets with Implications for the Origin of Life

Rocky planets may acquire a primordial atmosphere by the outgassing of volatiles from their magma ocean. The distribution of O between H2O, CO, and CO2 in chemical equilibrium subsequently changes significantly with decreasing temperature. We consider here two chemical models: one where CH4 and NH3 are assumed to be irrevocably destroyed by photolysis and second where these molecules persist. In the first case, we show that CO cannot coexist with H2O, since CO oxidizes at low temperatures to form CO2 and H2. In both cases, H escapes from the thermosphere within a few 10 million years by absorption of stellar XUV radiation. This escape drives an atmospheric self-oxidation process, whereby rocky planet atmospheres become dominated by CO2 and H2O regardless of their initial oxidation state at outgassing. HCN is considered a potential precursor of prebiotic compounds and RNA. Oxidizing atmospheres are inefficient at producing HCN by lightning. Alternatively, we have demonstrated that lightning-produced NO, which dissolves as nitrate in oceans, and interplanetary dust particles may be the main sources of fixed nitrogen in emerging biospheres. Our results highlight the need for origin-of-life scenarios where the first metabolism fixes its C from CO2, rather than from HCN and CO.

Insights from a dynamical system approach into the history of atmospheric oxygenation

Atmospheric oxygen levels are traditionally viewed to have been relatively stable throughout Earth's history with several-step increases. Emerging evidence, however, suggests extremely dynamic atmospheric oxygen levels through large swaths of Earth's history. Here, we provide a new perspective on atmospheric oxygen evolution using a dynamical analysis to explore the relative importance of previously proposed feedbacks on the global oxygen and carbon cycles. Our results from a stochastic analysis of oxygen mass balance in this framework suggest there are multiple steady states for atmospheric oxygen, but only three stable states. One stable state under anoxic conditions (<10-5 present atmospheric level (PAL)), one at low (~10-3to 10-2 PAL), and one near modern value atmospheric oxygen levels. Our findings also suggest two unstable states (tipping points) for atmospheric oxygen: one around 10-5 and another one around 10-1 PAL.

Mimicking lightning-induced electrochemistry on the early Earth

To test the hypothesis that an abiotic Earth and its inert atmosphere could form chemically reactive carbon- and nitrogen-containing compounds, we designed a plasma electrochemical setup to mimic lightning-induced electrochemistry under steady-state conditions of the early Earth. Air-gap electrochemical reactions at air-water-ground interfaces lead to remarkable yields, with up to 40 moles of carbon dioxide being reduced into carbon monoxide and formic acid, and 3 moles of gaseous nitrogen being fixed into nitrate, nitrite, and ammonium ions, per mole of transmitted electrons. Interfaces enable reactants (e.g., minerals) that may have been on land, in lakes, and in oceans to participate in radical and redox reactions, leading to higher yields compared to gas-phase-only reactions. Cloud-to-ground lightning strikes could have generated high concentrations of reactive molecules locally, establishing diverse feedstocks for early life to emerge and survive globally.

Ancient nitrogenases are ATP dependent

Life depends on a conserved set of chemical energy currencies that are relics of early biochemistry. One of these is ATP, a molecule that, when paired with a divalent metal ion such as Mg2+, can be hydrolyzed to support numerous cellular and molecular processes. Despite its centrality to extant biochemistry, it is unclear whether ATP supported the function of ancient enzymes. We investigate the evolutionary necessity of ATP by experimentally reconstructing an ancestral variant of the N2-reducing enzyme nitrogenase. The Proterozoic ancestor is predicted to be ~540-2,300 million years old, post-dating the Great Oxidation Event. Growth rates under nitrogen-fixing conditions are ~80% of those of wild type in Azotobacter vinelandii. In the extant enzyme, the hydrolysis of two MgATP is coupled to electron transfer to support substrate reduction. The ancestor has a strict requirement for ATP with no other nucleotide triphosphate analogs (GTP, ITP, and UTP) supporting activity. Alternative divalent metal ions (Fe2+, Co2+, and Mn2+) support activity with ATP but with diminished activities compared to Mg2+, similar to the extant enzyme. Additionally, it is shown that the ancestor has an identical efficiency in ATP hydrolyzed per electron transferred to the extant of two. Our results provide direct laboratory evidence of ATP usage by an ancient enzyme.IMPORTANCELife depends on energy-carrying molecules to power many sustaining processes. There is evidence that these molecules may predate the rise of life on Earth, but how and when these dependencies formed is unknown. The resurrection of ancient enzymes provides a unique tool to probe the enzyme's function and usage of energy-carrying molecules, shedding light on their biochemical origins. Through experimental reconstruction, this research investigates the ancestral dependence of a nitrogen-fixing enzyme on the energy carrier ATP, a requirement for function in the modern enzyme. We show that the resurrected ancestor does not have generalist nucleotide specificity. Rather, the ancestor has a strict requirement for ATP, like the modern enzyme, with similar function and efficiency. The findings elucidate the early-evolved necessity of energy-yielding molecules, delineating their role in ancient biochemical processes. Ultimately, these insights contribute to unraveling the intricate tapestry of evolutionary biology and the origins of life-sustaining dependencies.

Lateral redox variability in ca. 1.9 Ga marine environments indicated by organic carbon and nitrogen isotope compositions

The stepwise oxygenation of Earth's surficial environment is thought to have shaped the evolutionary history of life. Microfossil records and molecular clocks suggest eukaryotes appeared during the Paleoproterozoic, perhaps shortly after the Great Oxidation Episode at ca. 2.43 Ga. The mildly oxygenated atmosphere and surface oceans likely contributed to the early evolution of eukaryotes. However, the principal trigger for the eukaryote appearance and a potential factor for their delayed expansion (i.e., intermediate ocean redox conditions until the Neoproterozoic) remain poorly understood, largely owing to a lack of constraints on marine and terrestrial nutrient cycling. Here, we analyzed redox-sensitive element contents and organic carbon and nitrogen isotope compositions of relatively low metamorphic-grade (greenschist facies) black shales preserved in the Flin Flon Belt of central Canada to examine open-marine redox conditions and biological activity around the ca. 1.9 Ga Flin Flon oceanic island arc. The black shale samples were collected from the Reed Lake area in the eastern part of the Flin Flon Belt, and the depositional site was likely distal from the Archean cratons. The black shales have low Al/Ti ratios and are slightly depleted in light rare-earth elements relative to the post-Archean average shale, which is consistent with a limited contribution from felsic igneous rocks in Archean upper continental crust. Redox conditions have likely varied between suboxic and euxinic at the depositional site of the studied section, as suggested by variable U/Al and Mo/Al ratios. Organic carbon and nitrogen isotope compositions of the black shales are approximately -23‰ and +13.7‰, respectively, and these values are systematically higher than those of broadly coeval continental margin deposits (approximately -30‰ for δ13Corg and +5‰ for δ15Nbulk). These elevated values are indicative of high productivity that led to enhanced denitrification (i.e., a high denitrification rate relative to nitrogen influx at the depositional site). Similar geochemical patterns have also been observed in the modern Peruvian oxygen minimum zone where dissolved nitrogen compounds are actively lost from the reservoir via denitrification and anammox, but the large nitrate reservoir of the deep ocean prevents exhaustion of the surface nitrate pool. Nitrogen must have been widely bioavailable in the ca. 1.9 Ga oceans, and its supply to upwelling zones must have supported habitable environments for eukaryotes, even in the middle of oceans around island arcs.

Onset of coupled atmosphere-ocean oxygenation 2.3 billion years ago

The initial rise of molecular oxygen (O2) shortly after the Archaean-Proterozoic transition 2.5 billion years ago was more complex than the single step-change once envisioned. Sulfur mass-independent fractionation records suggest that the rise of atmospheric O2 was oscillatory, with multiple returns to an anoxic state until perhaps 2.2 billion years ago1-3. Yet few constraints exist for contemporaneous marine oxygenation dynamics, precluding a holistic understanding of planetary oxygenation. Here we report thallium (Tl) isotope ratio and redox-sensitive element data for marine shales from the Transvaal Supergroup, South Africa. Synchronous with sulfur isotope evidence of atmospheric oxygenation in the same shales3, we found lower authigenic 205Tl/203Tl ratios indicative of widespread manganese oxide burial on an oxygenated seafloor and higher redox-sensitive element abundances consistent with expanded oxygenated waters. Both signatures disappear when the sulfur isotope data indicate a brief return to an anoxic atmospheric state. Our data connect recently identified atmospheric O2 dynamics on early Earth with the marine realm, marking an important turning point in Earth's redox history away from heterogeneous and highly localized 'oasis'-style oxygenation.

Pyritic stromatolites from the Paleoarchean Dresser Formation, Pilbara Craton: Resolving biogenicity and hydrothermally influenced ecosystem dynamics

This study investigates the paleobiological significance of pyritic stromatolites from the 3.48 billion-year-old Dresser Formation, Pilbara Craton. By combining paleoenvironmental analyses with observations from well-preserved stromatolites in newly obtained drill cores, the research reveals stratiform and columnar to domal pyritic structures with wavy to wrinkly laminations and crest thickening, hosted within facies variably influenced by syn-depositional hydrothermal activity. The columnar and domal stromatolites occur in strata with clearly distinguishable primary depositional textures. Mineralogical variability and fine-scale interference textures between the microbialites and the enclosing sediment highlight interplays between microbial and depositional processes. The stromatolites consist of organomineralization - nanoporous pyrite and microspherulitic barite - hosting significant thermally mature organic matter (OM). This includes filamentous organic microstructures encased within nanoporous pyrite, resembling the extracellular polymeric substance (EPS) of microbes. These findings imply biogenicity and support the activity of microbial life in a volcano-sedimentary environment with hydrothermal activity and evaporative cycles. Coupled changes in stromatolite morphology and host facies suggest growth in diverse niches, from dynamic, hydrothermally influenced shallow-water environments to restricted brine pools strongly enriched inSO 4 2 - $$ {\mathrm{SO}}_4^{2-} $$ from seawater and hydrothermal activity. These observations, along with S stable isotope data indicating influence by S metabolisms, and accumulations of biologically significant metals and metalloids (Ni and As) within the microbialites, help constrain microbial processes. Columnar to domal stromatolites in dynamic, hydrothermally influenced shallow water deposits likely formed by microbial communities dominated by phototrophs. Stratiform pyritic structures within barite-rich strata may reflect the prevalence of chemotrophs near hydrothermal venting, where hydrothermal activity and microbial processes influenced barite precipitation. Rapid pyrite precipitation, a putative taphonomic process for preserving microbial remnants, is attributed to microbial sulfate reduction and reduced S sourced from hydrothermal activity. In conclusion, this research underscores the biogenicity of the Dresser stromatolites and advances our understanding of microbial ecosystems in Earth's early history.

Oxygenation of Earth's atmosphere induced metabolic and ecologic transformations recorded in the Lomagundi-Jatuli carbon isotopic excursion

The oxygenation of Earth's atmosphere represents the quintessential transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution; molecular clock models indicate the diversification and ecological expansion of respiratory metabolisms in the several hundred million years following atmospheric oxygenation. Across this same interval, the geological record preserves 13C enrichment in some carbonate rocks, called the Lomagundi-Jatuli excursion (LJE). By combining data from geologic and genomic records, a self-consistent metabolic evolution model emerges for the LJE. First, fermentation and methanogenesis were major processes remineralizing organic carbon before atmospheric oxygenation. Once an ozone layer formed, shallow water and exposed environments were shielded from UVB/C radiation, allowing the expansion of cyanobacterial primary productivity. High primary productivity and methanogenesis led to preferential removal of 12C into organic carbon and CH4. Extreme and variable 13C enrichments in carbonates were caused by 13C-depleted CH4 loss to the atmosphere. Through time, aerobic respiration diversified and became ecologically widespread, as did other new metabolisms. Respiration displaced fermentation and methanogenesis as the dominant organic matter remineralization processes. As CH4 loss slowed, dissolved inorganic carbon in shallow environments was no longer highly 13C enriched. Thus, the loss of extreme 13C enrichments in carbonates marks the establishment of a new microbial mat ecosystem structure, one dominated by respiratory processes distributed along steep redox gradients. These gradients allowed the exchange of metabolic by-products among metabolically diverse organisms, providing novel metabolic opportunities. Thus, the microbially induced oxygenation of Earth's atmosphere led to the transformation of microbial ecosystems, an archetypal example of planetary microbiology.IMPORTANCEThe oxygenation of Earth's atmosphere represents the most extensive known chemical transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution by providing oxidants independent of the sites of photosynthesis. Thus, the evolutionary changes during this interval and their effects on planetary-scale biogeochemical cycles are fundamental to our understanding of the interdependencies among genomes, organisms, ecosystems, elemental cycles, and Earth's surface chemistry through time.

Enigmatic evolution of microbial nitrogen fixation: insights from Earth's past

The evolution of nitrogen fixation undoubtedly altered nearly all corners of the biosphere, given the essential role of nitrogen in the synthesis of biomass. To date, there is no unified view on what planetary conditions gave rise to nitrogen fixation or how these conditions have sustained it evolutionarily. Intriguingly, the concentrations of metals that nitrogenases require to function have changed throughout Earth's history. In this review, we describe the interconnection of the metal and nitrogen cycles with nitrogenase evolution and the importance of ancient ecology in the formation of the modern nitrogen cycle. We argue that exploration of the nitrogen cycle's deep past will provide insights into humanity's immediate environmental challenges centered on nitrogen availability.

The origin and evolution of Earth's nitrogen

Nitrogen is a vital element for life on Earth. Its cycling between the surface (atmosphere + crust) and the mantle has a profound influence on the atmosphere and climate. However, our understanding of the origin and evolution of Earth's nitrogen is still incomplete. This review presents an overview of the current understanding of Earth's nitrogen budget and the isotope composition of different reservoirs, laboratory constraints on deep nitrogen geochemistry, and our understanding of the origin of Earth's nitrogen and the deep nitrogen cycle through plate subduction and volcanism. The Earth may have acquired its nitrogen heterogeneously during the main accretion phase, initially from reduced, enstatite-chondrite-like impactors, and subsequently from increasingly oxidized impactors and minimal CI-chondrite-like materials. Like Earth's surface, the mantle and core are also significant nitrogen reservoirs. The nitrogen abundance and isotope composition of these three reservoirs may have been fundamentally established during the main accretion phase and have been insignificantly modified afterwards by the deep nitrogen cycle, although there is a net nitrogen ingassing into Earth's mantle in modern subduction zones. However, it is estimated that the early atmosphere of Earth may have contained ∼1.4 times the present-day atmospheric nitrogen (PAN), with ∼0.4 PAN being sequestered into the crust via biotic nitrogen fixation. In order to gain a better understanding of the origin and evolution of Earth's nitrogen, directions for future research are suggested.

Atmospheric oxygenation as a potential trigger for climate cooling

Secular changes in atmospheric CO2 and consequent global climate variations, are commonly attributed to global outgassing and the efficiency of silicate weathering, which may have been linked to mountain formation, land/arc distribution, and plant colonization through geological time. Although oxidative weathering has been shown to exert a significant role in the propagation of weathering fronts through the oxidation of Fe-bearing minerals, the influence of atmospheric O2 concentration (pO2) on silicate weathering, CO2 consumption, and global climate has not been thoroughly evaluated. This study presents a numerical model aimed at estimating the effects of pO2 on the climate, considering the influence of pO2 on the regolith thickness and thus weathering duration of granitic domains. Our model simulations reveal that an increase in weathering efficiency, through deeper penetration of the oxidative weathering front in the granitic regolith, would independently introduce a steady-state climate cooling of up to ∼8 °C, in step with one-order of magnitude rise in pO2. This temperature change may have repeatedly initiated the runaway ice-albedo feedback, leading to global glacial events (e.g., Neoproterozoic Snowball Earth). Increasing granitic weathering efficiency caused by a substantial pO2 increase may also have contributed to the development of icehouse climate during the Phanerozoic.

Primitive purine biosynthesis connects ancient geochemistry to modern metabolism

An unresolved question in the origin and evolution of life is whether a continuous path from geochemical precursors to the majority of molecules in the biosphere can be reconstructed from modern-day biochemistry. Here we identified a feasible path by simulating the evolution of biosphere-scale metabolism, using only known biochemical reactions and models of primitive coenzymes. We find that purine synthesis constitutes a bottleneck for metabolic expansion, which can be alleviated by non-autocatalytic phosphoryl coupling agents. Early phases of the expansion are enriched with enzymes that are metal dependent and structurally symmetric, supporting models of early biochemical evolution. This expansion trajectory suggests distinct hypotheses regarding the tempo, mode and timing of metabolic pathway evolution, including a late appearance of methane metabolisms and oxygenic photosynthesis consistent with the geochemical record. The concordance between biological and geological analyses suggests that this trajectory provides a plausible evolutionary history for the vast majority of core biochemistry.

The paleoredox context of early eukaryotic evolution: insights from the Tonian Mackenzie Mountains Supergroup, Canada

Tonian (ca. 1000-720 Ma) marine environments are hypothesised to have experienced major redox changes coinciding with the evolution and diversification of multicellular eukaryotes. In particular, the earliest Tonian stratigraphic record features the colonisation of benthic habitats by multicellular macroscopic algae, which would have been powerful ecosystem engineers that contributed to the oxygenation of the oceans and the reorganisation of biogeochemical cycles. However, the paleoredox context of this expansion of macroalgal habitats in Tonian nearshore marine environments remains uncertain due to limited well-preserved fossils and stratigraphy. As such, the interdependent relationship between early complex life and ocean redox state is unclear. An assemblage of macrofossils including the chlorophyte macroalga Archaeochaeta guncho was recently discovered in the lower Mackenzie Mountains Supergroup in Yukon (Canada), which archives marine sedimentation from ca. 950-775 Ma, permitting investigation into environmental evolution coincident with eukaryotic ecosystem evolution and expansion. Here we present multi-proxy geochemical data from the lower Mackenzie Mountains Supergroup to constrain the paleoredox environment within which these large benthic macroalgae thrived. Two transects show evidence for basin-wide anoxic (ferruginous) oceanic conditions (i.e., high FeHR/FeT, low Fepy/FeHR), with muted redox-sensitive trace metal enrichments and possible seasonal variability. However, the weathering of sulfide minerals in the studied samples may obscure geochemical signatures of euxinic conditions. These results suggest that macroalgae colonized shallow environments in an ocean that remained dominantly anoxic with limited evidence for oxygenation until ca. 850 Ma. Collectively, these geochemical results provide novel insights into the environmental conditions surrounding the evolution and expansion of benthic macroalgae and the eventual dominance of oxygenated oceanic conditions required for the later emergence of animals.

From cyanobacteria and cyanophages to chloroplasts: the fate of the genomes of oxyphototrophs and the genes encoding photosystem II proteins

Chloroplasts are the result of endosymbiosis of cyanobacterial organisms with proto-eukaryotes. The psbA, psbD and psbO genes are present in all oxyphototrophs and encode the D1/D2 proteins of photosystem II (PSII) and PsbO, respectively. PsbO is a peripheral protein that stabilizes the O2-evolving complex in PSII. Of these genes, psbA and psbD remained in the chloroplastic genome, while psbO was transferred to the nucleus. The genomes of selected cyanobacteria, chloroplasts and cyanophages carrying psbA and psbD, respectively, were analysed. The highest density of genes and coding sequences (CDSs) was estimated for the genomes of cyanophages, cyanobacteria and chloroplasts. The synonymous mutation rate (rS) of psbA and psbD in chloroplasts remained almost unchanged and is lower than that of psbO. The results indicate that the decreasing genome size in chloroplasts is more similar to the genome reduction observed in contemporary endosymbiotic organisms than in streamlined genomes of free-living cyanobacteria. The rS of atpA, which encodes the α-subunit of ATP synthase in chloroplasts, suggests that psbA and psbD, and to a lesser extent psbO, are ancient and conservative and arose early in the evolution of oxygenic photosynthesis. The role of cyanophages in the evolution of oxyphototrophs and chloroplastic genomes is discussed.

Comments on "was hydrogen peroxide present before the arrival of oxygenic photosynthesis? The important role of iron(II) in the archean ocean"

Recent research has hypothesized that hydrogen peroxide (H2O2) may have emerged from abiotic geochemical processes during the Archean eon (4.0-2.5 Ga), stimulating the evolution of an enzymatic antioxidant system in early life. This eventually led to the evolution of cyanobacteria, and in turn, the accumulation of oxygen on Earth. In the latest issue of Redox Biology, Koppenol and Sies (vol. 29, no. 103012, 2024) argued against this hypothesis and suggested instead that early organisms would not have been exposed to H2O2 due to its short half-life in the ferruginous oceans of the Archean. We find these arguments to be factually incomplete because they do not consider that freshwater or some coastal marine environments during the Archean could indeed have led to H2O2 generation and accumulation. In these environments, abiotic oxidants could have interacted with early life, thus steering its evolutionary course.

Nitric oxide sensor NsrR is the key direct regulator of magnetosome formation and nitrogen metabolism in Magnetospirillum

Nitric oxide (NO) plays an essential role as signaling molecule in regulation of eukaryotic biomineralization, but its role in prokaryotic biomineralization is unknown. Magnetospirillum gryphiswaldense MSR-1, a model strain for studies of prokaryotic biomineralization, has the unique ability to form magnetosomes (magnetic organelles). We demonstrate here that magnetosome biomineralization in MSR-1 requires the presence of NsrRMg (an NO sensor) and a certain level of NO. MSR-1 synthesizes endogenous NO via nitrification-denitrification pathway to activate magnetosome formation. NsrRMg was identified as a global transcriptional regulator that acts as a direct activator of magnetosome gene cluster (MGC) and nitrification genes but as a repressor of denitrification genes. Specific levels of NO modulate DNA-binding ability of NsrRMg to various target promoters, leading to enhancing expression of MGC genes, derepressing denitrification genes, and repressing nitrification genes. These regulatory functions help maintain appropriate endogenous NO level. This study identifies for the first time the key transcriptional regulator of major MGC genes, clarifies the molecular mechanisms underlying NsrR-mediated NO signal transduction in magnetosome formation, and provides a basis for a proposed model of the role of NO in the evolutionary origin of prokaryotic biomineralization processes.

Spatiotemporal Characteristics Determining the Multifaceted Nature of Reactive Oxygen, Nitrogen, and Sulfur Species in Relation to Proton Homeostasis

Significance: Reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS) act as signaling molecules, regulating gene expression, enzyme activity, and physiological responses. However, excessive amounts of these molecular species can lead to deleterious effects, causing cellular damage and death. This dual nature of ROS, RNS, and RSS presents an intriguing conundrum that calls for a new paradigm. Recent Advances: Recent advancements in the study of photosynthesis have offered significant insights at the molecular level and with high temporal resolution into how the photosystem II oxygen-evolving complex manages to prevent harmful ROS production during the water-splitting process. These findings suggest that a dynamic spatiotemporal arrangement of redox reactions, coupled with strict regulation of proton transfer, is crucial for minimizing unnecessary ROS formation. Critical Issues: To better understand the multifaceted nature of these reactive molecular species in biology, it is worth considering a more holistic view that combines ecological and evolutionary perspectives on ROS, RNS, and RSS. By integrating spatiotemporal perspectives into global, cellular, and biochemical events, we discuss local pH or proton availability as a critical determinant associated with the generation and action of ROS, RNS, and RSS in biological systems. Future Directions: The concept of localized proton availability will not only help explain the multifaceted nature of these ubiquitous simple molecules in diverse systems but also provide a basis for new therapeutic strategies to manage and manipulate these reactive species in neural disorders, pathogenic diseases, and antiaging efforts.

The reproduction process of Gram-positive protocells

Protocells are believed to have existed on early Earth prior to the emergence of prokaryotes. Due to their rudimentary nature, it is widely accepted that these protocells lacked intracellular mechanisms to regulate their reproduction, thereby relying heavily on environmental conditions. To understand protocell reproduction, we adopted a top-down approach of transforming a Gram-positive bacterium into a lipid-vesicle-like state. In this state, cells lacked intrinsic mechanisms to regulate their morphology or reproduction, resembling theoretical propositions on protocells. Subsequently, we grew these proxy-protocells under the environmental conditions of early Earth to understand their impact on protocell reproduction. Despite the lack of molecular biological coordination, cells in our study underwent reproduction in an organized manner. The method and the efficiency of their reproduction can be explained by an interplay between the physicochemical properties of cell constituents and environmental conditions. While the overall reproductive efficiency in these top-down modified cells was lower than their counterparts with a cell wall, the process always resulted in viable daughter cells. Given the simplicity and suitability of this reproduction method to early Earth environmental conditions, we propose that primitive protocells likely reproduced by a process like the one we described below.

Chapter 4: A Geological and Chemical Context for the Origins of Life on Early Earth

Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on 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.

Transcriptomic and photosynthetic analyses of Synechocystis sp. PCC6803 and Chlorogloeopsis fritschii sp. PCC6912 exposed to an M-dwarf spectrum under an anoxic atmosphere

Introduction

Cyanobacteria appeared in the anoxic Archean Earth, evolving for the first time oxygenic photosynthesis and deeply changing the atmosphere by introducing oxygen. Starting possibly from UV-protected environments, characterized by low visible and far-red enriched light spectra, cyanobacteria spread everywhere on Earth thanks to their adaptation capabilities in light harvesting. In the last decade, few cyanobacteria species which can acclimate to far-red light through Far-Red Light Photoacclimation (FaRLiP) have been isolated. FaRLiP cyanobacteria were thus proposed as model organisms to study the origin of oxygenic photosynthesis as well as its possible functionality around stars with high far-red emission, the M-dwarfs. These stars are astrobiological targets, as their longevity could sustain life evolution and they demonstrated to host rocky terrestrial-like exoplanets within their Habitable Zone.

Methods

We studied the acclimation responses of the FaRLiP strain Chlorogloeopsis fritschii sp. PCC6912 and the non-FaRLiP strain Synechocystis sp. PCC6803 to the combination of three simulated light spectra (M-dwarf, solar and far-red) and two atmospheric compositions (oxic, anoxic). We first checked their growth, O2 production and pigment composition, then we studied their transcriptional responses by RNA sequencing under each combination of light spectrum and atmosphere conditions.

Results and discussion

PCC6803 did not show relevant differences in gene expression when comparing the responses to M-dwarf and solar-simulated lights, while far-red caused a variation in the transcriptional level of many genes. PCC6912 showed, on the contrary, different transcriptional responses to each light condition and activated the FaRLiP response under the M-dwarf simulated light. Surprisingly, the anoxic atmosphere did not impact the transcriptional profile of the 2 strains significantly. Results show that both cyanobacteria seem inherently prepared for anoxia and to harvest the photons emitted by a simulated M-dwarf star, whether they are only visible (PCC6803) or also far-red photons (PCC6912). They also show that visible photons in the simulated M-dwarf are sufficient to keep a similar metabolism with respect to solar-simulated light.

Conclusion

Results prove the adaptability of the cyanobacterial metabolism and enhance the plausibility of finding oxygenic biospheres on exoplanets orbiting M-dwarf stars.

Modern analogs for ammonia flux from terrestrial hydrothermal features to the Archean atmosphere

The isotopic composition of nitrogen in the rock record provides valuable evidence of reactive nitrogen sources and processing on early Earth, but the wide range of δ15N values (- 10.2 to + 50.4‰) leads to ambiguity in defining the early Precambrian nitrogen cycle. The high δ15N values have been explained by large fractionation associated with the onset of nitrification and/or fractionation produced by ammonia-ammonium equilibrium and water-air flux in alkaline paleolakes. Previous flux sensitivity studies in modern water bodies report alkaline pH is not a prerequisite and temperature can be the dominate parameter driving water-air flux. Here, I use the chemical and physical components of 1022 modern hydrothermal features to provide evidence that water-air NH3 flux produced a significant source of fixed nitrogen to early Earth's atmosphere and biosphere. With regard to the modeled average NH3 flux (2.1 kg N m-2 year-1) and outlier removed average flux (1.2 kg N m-2 year-1), the Archean Earth's surface would need to be 0.0092, and 0.017% terrestrial hydrothermal features, respectively, for the flux to match the annual amount of N produced by biogenic fixation on modern Earth. Water-air NH3 flux from terrestrial hydrothermal features may have played a significant role in supplying bioavailable nitrogen to early life.

Natural ocean iron fertilization and climate variability over geological periods

Marine primary producers are largely dependent on and shape the Earth's climate, although their relationship with climate varies over space and time. The growth of phytoplankton and associated marine primary productivity in most of the modern global ocean is limited by the supply of nutrients, including the micronutrient iron. The addition of iron via episodic and frequent events drives the biological carbon pump and promotes the sequestration of atmospheric carbon dioxide (CO2 ) into the ocean. However, the dependence between iron and marine primary producers adaptively changes over different geological periods due to the variation in global climate and environment. In this review, we examined the role and importance of iron in modulating marine primary production during some specific geological periods, that is, the Great Oxidation Event (GOE) during the Huronian glaciation, the Snowball Earth Event during the Cryogenian, the glacial-interglacial cycles during the Pleistocene, and the period from the last glacial maximum to the late Holocene. Only the change trend of iron bioavailability and climate in the glacial-interglacial cycles is consistent with the Iron Hypothesis. During the GOE and the Snowball Earth periods, although the bioavailability of iron in the ocean and the climate changed dramatically, the changing trend of many factors contradicted the Iron Hypothesis. By detangling the relationship among marine primary productivity, iron availability and oceanic environments in different geological periods, this review can offer some new insights for evaluating the impact of ocean iron fertilization on removing CO2 from the atmosphere and regulating the climate.

Methanol on the rocks: green rust transformation promotes the oxidation of methane

Shared coordination geometries between metal ions within reactive minerals and enzymatic metal cofactors hints at mechanistic and possibly evolutionary homology between particular abiotic chemical mineralogies and biological metabolism. The octahedral coordination of reactive Fe2+/3+ minerals such as green rusts, endemic to anoxic sediments and the early Earth's oceans, mirrors the di-iron reaction centre of soluble methane monooxygenase (sMMO), responsible for methane oxidation in methanotrophy. We show that methane oxidation occurs in tandem with the oxidation of green rust to lepidocrocite and magnetite, mimicking radical-mediated methane oxidation found in sMMO to yield not only methanol but also halogenated hydrocarbons in the presence of seawater. This naturally occurring geochemical pathway for CH4 oxidation elucidates a previously unidentified carbon cycling mechanism in modern and ancient environments and reveals clues into mineral-mediated reactions in the synthesis of organic compounds necessary for the emergence of life.

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.

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.

On the potential roles of phosphorus in the early evolution of energy metabolism

Energy metabolism in extant life is centered around phosphate and the energy-dense phosphoanhydride bonds of adenosine triphosphate (ATP), a deeply conserved and ancient bioenergetic system. Yet, ATP synthesis relies on numerous complex enzymes and has an autocatalytic requirement for ATP itself. This implies the existence of evolutionarily simpler bioenergetic pathways and potentially primordial alternatives to ATP. The centrality of phosphate in modern bioenergetics, coupled with the energetic properties of phosphorylated compounds, may suggest that primordial precursors to ATP also utilized phosphate in compounds such as pyrophosphate, acetyl phosphate and polyphosphate. However, bioavailable phosphate may have been notably scarce on the early Earth, raising doubts about the roles that phosphorylated molecules might have played in the early evolution of life. A largely overlooked phosphorus redox cycle on the ancient Earth might have provided phosphorus and energy, with reduced phosphorus compounds potentially playing a key role in the early evolution of energy metabolism. Here, we speculate on the biological phosphorus compounds that may have acted as primordial energy currencies, sources of environmental energy, or sources of phosphorus for the synthesis of phosphorylated energy currencies. This review encompasses discussions on the evolutionary history of modern bioenergetics, and specifically those pathways with primordial relevance, and the geochemistry of bioavailable phosphorus on the ancient Earth. We highlight the importance of phosphorus, not only in the form of phosphate, to early biology and suggest future directions of study that may improve our understanding of the early evolution of bioenergetics.

Methane formation driven by light and heat prior to the origin of life and beyond

Methane is a potent greenhouse gas, which likely enabled the evolution of life by keeping the early Earth warm. Here, we demonstrate routes towards abiotic methane and ethane formation under early-earth conditions from methylated sulfur and nitrogen compounds with prebiotic origin. These compounds are demethylated in Fenton reactions governed by ferrous iron and reactive oxygen species (ROS) produced by light and heat in aqueous environments. After the emergence of life, this phenomenon would have greatly intensified in the anoxic Archean by providing methylated sulfur and nitrogen substrates. This ROS-driven Fenton chemistry can occur delocalized from serpentinization across Earth's humid realm and thereby substantially differs from previously suggested methane formation routes that are spatially restricted. Here, we report that Fenton reactions driven by light and heat release methane and ethane and might have shaped the chemical evolution of the atmosphere prior to the origin of life and beyond.

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.

Iron or sulfur respiration-an adaptive choice determining the fitness of a natronophilic bacterium Dethiobacter alkaliphilus in geochemically contrasting environments

Haloalkaliphilic microorganisms are double extremophiles functioning optimally at high salinity and pH. Their typical habitats are soda lakes, geologically ancient yet widespread ecosystems supposed to harbor relict microbial communities. We compared metabolic features and their determinants in two strains of the natronophilic species Dethiobacter alkaliphilus, the only cultured representative of the class "Dethiobacteria" (Bacillota). The strains of D. alkaliphilus were previously isolated from geographically remote Mongolian and Kenyan soda lakes. The type strain AHT1^T was described as a facultative chemolithoautotrophic sulfidogen reducing or disproportionating sulfur or thiosulfate, while strain Z-1002 was isolated as a chemolithoautotrophic iron reducer. Here, we uncovered the iron reducing ability of strain AHT1^T and the ability of strain Z-1002 for thiosulfate reduction and anaerobic Fe(II) oxidation. Key catabolic processes sustaining the growth of both D. alkaliphilus strains appeared to fit the geochemical settings of two contrasting natural alkaline environments, sulfur-enriched soda lakes and iron-enriched serpentinites. This hypothesis was supported by a meta-analysis of Dethiobacterial genomes and by the enrichment of a novel phylotype from a subsurface alkaline aquifer under Fe(III)-reducing conditions. Genome analysis revealed multiheme c-type cytochromes to be the most probable determinants of iron and sulfur redox transformations in D. alkaliphilus. Phylogeny reconstruction showed that all the respiratory processes in this organism are likely provided by evolutionarily related early forms of unconventional octaheme tetrathionate and sulfite reductases and their structural analogs, OmhA/OcwA Fe(III)-reductases. Several phylogenetically related determinants of anaerobic Fe(II) oxidation were identified in the Z-1002 genome, and the oxidation process was experimentally demonstrated. Proteomic profiling revealed two distinct sets of multiheme cytochromes upregulated in iron(III)- or thiosulfate-respiring cells and the cytochromes peculiar for Fe(II) oxidizing cells. We suggest that maintaining high variation in multiheme cytochromes is an effective adaptive strategy to occupy geochemically contrasting alkaline environments. We propose that sulfur-enriched soda lakes could be secondary habitats for D. alkaliphilus compared to Fe-rich serpentinites, and that the ongoing evolution of Dethiobacterales could retrace the evolutionary path that may have occurred in prokaryotes at a turning point in the biosphere's history, when the intensification of the sulfur cycle outweighed the global significance of the iron cycle.

Why the day is 24 hours long: The history of Earth's atmospheric thermal tide, composition, and mean temperature

The Sun drives a semidiurnal (12-hour) thermal tide in Earth's atmosphere. Zahnle and Walker suggested that an atmospheric oscillation with period P_res ≈ 10.5 hours resonated with the Solar driving ≈600 million years ago (Ma), when the length of day (lod) was ≈21 hours. They argued that the enhanced torque balanced the Lunar tidal torque, fixing the lod. We explore this hypothesis using two different global circulation models (GCMs), finding P_res = 11.4 and 11.5 hours today, in excellent agreement with a recent measurement. We quantify the relation between P_res, mean surface temperature [Formula: see text], composition, and Solar luminosity. We use geologic data, a dynamical model, and a Monte Carlo sampler to find possible histories for the Earth-Moon system. In the most likely model, the lod was fixed at ≈19.5 hours between 2200 and 600 Ma ago, with sustained high [Formula: see text] and an increase in the angular momentum L_EM of the Earth-Moon system of ≈5%.

Solar energy conversion by photosystem II: principles and structures

Photosynthetic water oxidation by Photosystem II (PSII) is a fascinating process because it sustains life on Earth and serves as a blue print for scalable synthetic catalysts required for renewable energy applications. The biophysical, computational, and structural description of this process, which started more than 50 years ago, has made tremendous progress over the past two decades, with its high-resolution crystal structures being available not only of the dark-stable state of PSII, but of all the semi-stable reaction intermediates and even some transient states. Here, we summarize the current knowledge on PSII with emphasis on the basic principles that govern the conversion of light energy to chemical energy in PSII, as well as on the illustration of the molecular structures that enable these reactions. The important remaining questions regarding the mechanism of biological water oxidation are highlighted, and one possible pathway for this fundamental reaction is described at a molecular level.

Mineral-Bound Trace Metals as Cofactors for Anaerobic Biological Nitrogen Fixation

Nitrogenase is the only known biological enzyme capable of reducing N₂ to bioavailable NH₃. Most nitrogenases use Mo as a metallocofactor, while alternative cofactors V and Fe are also viable. Both geological and bioinformatic evidence suggest an ancient origin of Mo-based nitrogenase in the Archean, despite the low concentration of dissolved Mo in the Archean oceans. This apparent paradox would be resolvable if mineral-bound Mo were bioavailable for nitrogen fixation by ancient diazotrophs. In this study, the bioavailability of mineral-bound Mo, V, and Fe was determined by incubating an obligately anaerobic diazotroph Clostridium kluyveri with Mo-, V-, and Fe-bearing minerals (molybdenite, cavansite, and ferrihydrite, respectively) and basalt under diazotrophic conditions. The results showed that C. kluyveri utilized mineral-associated metals to express nitrogenase genes and fix nitrogen, as measured by the reverse transcription quantitative polymerase chain reaction and acetylene reduction assay, respectively. C. kluyveri secreted chelating molecules to extract metals from the minerals. As a result of microbial weathering, mineral surface chemistry significantly changed, likely due to surface coating by microbial exudates for metal extraction. These results provide important support for the ancient origin of Mo-based nitrogenase, with profound implications for coevolution of the biosphere and geosphere.

Effects of RuBisCO and CO2 concentration on cyanobacterial growth and carbon isotope fractionation

Carbon isotope biosignatures preserved in the Precambrian geologic record are primarily interpreted to reflect ancient cyanobacterial carbon fixation catalyzed by Form I RuBisCO enzymes. The average range of isotopic biosignatures generally follows that produced by extant cyanobacteria. However, this observation is difficult to reconcile with several environmental (e.g., temperature, pH, and CO₂ concentrations), molecular, and physiological factors that likely would have differed during the Precambrian and can produce fractionation variability in contemporary organisms that meets or exceeds that observed in the geologic record. To test a specific range of genetic and environmental factors that may impact ancient carbon isotope biosignatures, we engineered a mutant strain of the model cyanobacterium Synechococcus elongatus PCC 7942 that overexpresses RuBisCO across varying atmospheric CO₂ concentrations. We hypothesized that changes in RuBisCO expression would impact the net rates of intracellular CO₂ fixation versus CO₂ supply, and thus whole-cell carbon isotope discrimination. In particular, we investigated the impacts of RuBisCO overexpression under changing CO₂ concentrations on both carbon isotope biosignatures and cyanobacterial physiology, including cell growth and oxygen evolution rates. We found that an increased pool of active RuBisCO does not significantly affect the ¹³ C/¹² C isotopic discrimination (ε_p ) at all tested CO₂ concentrations, yielding ε_p of ≈ 23‰ for both wild-type and mutant strains at elevated CO₂ . We therefore suggest that expected variation in cyanobacterial RuBisCO expression patterns should not confound carbon isotope biosignature interpretation. A deeper understanding of environmental, evolutionary, and intracellular factors that impact cyanobacterial physiology and isotope discrimination is crucial for reconciling microbially driven carbon biosignatures with those preserved in the geologic record.

Formation of Amino Acids and Carboxylic Acids in Weakly Reducing Planetary Atmospheres by Solar Energetic Particles from the Young Sun

Life most likely started during the Hadean Eon; however, the environmental conditions which contributed to the complexity of its chemistry are poorly known. A better understanding of various environmental conditions, including global (heliospheric) and local (atmospheric, surface, and oceanic), along with the internal dynamic conditions of the early Earth, are required to understand the onset of abiogenesis. Herein, we examine the contributions of galactic cosmic rays (GCRs) and solar energetic particles (SEPs) associated with superflares from the young Sun to the formation of amino acids and carboxylic acids in weakly reduced gas mixtures representing the early Earth's atmosphere. We also compare the products with those introduced by lightning events and solar ultraviolet light (UV). In a series of laboratory experiments, we detected and characterized the formation of amino acids and carboxylic acids via proton irradiation of a mixture of carbon dioxide, methane, nitrogen, and water in various mixing ratios. These experiments show the detection of amino acids after acid hydrolysis when 0.5% (v/v) of initial methane was introduced to the gas mixture. In the set of experiments with spark discharges (simulation of lightning flashes) performed for the same gas mixture, we found that at least 15% methane was required to detect the formation of amino acids, and no amino acids were detected in experiments via UV irradiation, even when 50% methane was used. Carboxylic acids were formed in non-reducing gas mixtures (0% methane) by proton irradiation and spark discharges. Hence, we suggest that GCRs and SEP events from the young Sun represent the most effective energy sources for the prebiotic formation of biologically important organic compounds from weakly reducing atmospheres. Since the energy flux of space weather, which generated frequent SEPs from the young Sun in the first 600 million years after the birth of the solar system, was expected to be much greater than that of GCRs, we conclude that SEP-driven energetic protons are the most promising energy sources for the prebiotic production of bioorganic compounds in the atmosphere of the Hadean Earth.

Insights into Early Steps of Decanoic Acid Self-Assemblies under Prebiotic Temperatures Using Molecular Dynamics Simulations

The origin of life possibly required processes in confined systems that facilitated simple chemical reactions and other more complex reactions impossible to achieve under the condition of infinite dilution. In this context, the self-assembly of micelles or vesicles derived from prebiotic amphiphilic molecules is a cornerstone in the chemical evolution pathway. A prime example of these building blocks is decanoic acid, a short-chain fatty acid capable of self-assembling under ambient conditions. This study explored a simplified system made of decanoic acids under temperatures ranging from 0 °C to 110 °C to replicate prebiotic conditions. The study revealed the first point of aggregation of decanoic acid into vesicles and examined the insertion of a prebiotic-like peptide in a primitive bilayer. The information gathered from this research provides critical insights into molecule interactions with primitive membranes, allowing us to understand the first nanometric compartments needed to trigger further reactions that were essential for the origin of life.

SO2 Photodissociation at 193 nm Directly Forms S(3P) + O2(3Σg-): Implications for the Archean Atmosphere on Earth

It is well-documented that photodissociation of SO₂ at λ = 193 nm produces O(³P_j) + SO X(³Σ^-). We provide experimental evidence of a new product channel from one-photon absorption producing S(³P_j) + O₂ X(³Σ_g^-) in 2-4% yield. We probe the reactant and all products with time-resolved photoelectron photoion coincidence spectroscopy. High-level ab initio calculations suggest that the new product channel can only occur on the ground-state potential energy surface through internal conversion from the excited state, followed by isomerization to a transient SOO intermediate. Classical trajectories on the ground-state potential energy surface with random initial conditions qualitatively reproduce the experimental yields. This unexpected photodissociation pathway may help reconcile discrepancies in sulfur mass-independent fractionation mechanisms in Earth's geologic history, which shape our understanding of the Archean atmosphere and the Great Oxygenation Event in Earth's evolution.

Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles

The dimethyl sulfoxide reductase (or MopB) family is a diverse assemblage of enzymes found throughout Bacteria and Archaea. Many of these enzymes are believed to have been present in the last universal common ancestor (LUCA) of all cellular lineages. However, gaps in knowledge remain about how MopB enzymes evolved and how this diversification of functions impacted global biogeochemical cycles through geologic time. In this study, we perform maximum likelihood phylogenetic analyses on manually curated comparative genomic and metagenomic data sets containing over 47,000 distinct MopB homologs. We demonstrate that these enzymes constitute a catalytically and mechanistically diverse superfamily defined not by the molybdopterin- or tungstopterin-containing [molybdopterin or tungstopterin bis(pyranopterin guanine dinucleotide) (Mo/W-bisPGD)] cofactor but rather by the structural fold that binds it in the protein. Our results suggest that major metabolic innovations were the result of the loss of the metal cofactor or the gain or loss of protein domains. Phylogenetic analyses also demonstrated that formate oxidation and CO2 reduction were the ancestral functions of the superfamily, traits that have been vertically inherited from the LUCA. Nearly all of the other families, which drive all other biogeochemical cycles mediated by this superfamily, originated in the bacterial domain. Thus, organisms from Bacteria have been the key drivers of catalytic and biogeochemical innovations within the superfamily. The relative ordination of MopB families and their associated catalytic activities emphasize fundamental mechanisms of evolution in this superfamily. Furthermore, it underscores the importance of prokaryotic adaptability in response to the transition from an anoxic to an oxidized atmosphere. IMPORTANCE The MopB superfamily constitutes a repertoire of metalloenzymes that are central to enduring mysteries in microbiology, from the origin of life and how microorganisms and biogeochemical cycles have coevolved over deep time to how anaerobic life adapted to increasing concentrations of O2 during the transition from an anoxic to an oxic world. Our work emphasizes that phylogenetic analyses can reveal how domain gain or loss events, the acquisition of novel partner subunits, and the loss of metal cofactors can stimulate novel radiations of enzymes that dramatically increase the catalytic versatility of superfamilies. We also contend that the superfamily concept in protein evolution can uncover surprising kinships between enzymes that have remarkably different catalytic and physiological functions.

Chronic Ionizing Radiation of Plants: An Evolutionary Factor from Direct Damage to Non-Target Effects

In present times, the levels of ionizing radiation (IR) on the surface of Earth are relatively low, posing no high challenges for the survival of contemporary life forms. IR derives from natural sources and naturally occurring radioactive materials (NORM), the nuclear industry, medical applications, and as a result of radiation disasters or nuclear tests. In the current review, we discuss modern sources of radioactivity, its direct and indirect effects on different plant species, and the scope of the radiation protection of plants. We present an overview of the molecular mechanisms of radiation responses in plants, which leads to a tempting conjecture of the evolutionary role of IR as a limiting factor for land colonization and plant diversification rates. The hypothesis-driven analysis of available plant genomic data suggests an overall DNA repair gene families' depletion in land plants compared to ancestral groups, which overlaps with a decrease in levels of radiation exposure on the surface of Earth millions of years ago. The potential contribution of chronic IR as an evolutionary factor in combination with other environmental factors is discussed.

Using thermodynamics to obtain geochemical information from genomes

Thermodynamic characterization of the relative stabilities of chemical compounds is a pillar of conceptual models in various fields of geosciences. Analogous models applied to genomes can yield new information about the relationship between genomes and their geochemical environments. In this perspective article, we present a chemical and thermodynamic analysis of prokaryotic lineages that have been the target of previous phylogenomic studies of evolutionary adaptation to varying redox conditions. The thermodynamic model development begins by quantifying the effects of hydrogen activity (aH₂ ) and temperature on the relative stabilities of organic compounds with different carbon oxidation state. When applied to proteins instead of metabolites, the same techniques can be used to identify combinations of aH₂ and temperature at which reference proteomes for Class I or Class II methanogens are relatively stable. The calculated aH₂ values are compatible with reported measurements for habitats of methanogens ranging from highly reducing submarine hydrothermal systems to less reducing environments including methanogenic sediments. In contrast to the transition between the two classes of methanogenic archaea, that between basal and terrestrial groups of Thaumarchaeota (denoting the origin of ammonia-oxidizing archaea) occurs at a less-reducing redox boundary. These examples reveal the consequences of energy minimization driving evolution and show how geochemical calculations involving biomolecules can be used to quantify and better understand the coevolution of the geosphere and biosphere.

Nitrogenase resurrection and the evolution of a singular enzymatic mechanism

The planetary biosphere is powered by a suite of key metabolic innovations that emerged early in the history of life. However, it is unknown whether life has always followed the same set of strategies for performing these critical tasks. Today, microbes access atmospheric sources of bioessential nitrogen through the activities of just one family of enzymes, nitrogenases. Here, we show that the only dinitrogen reduction mechanism known to date is an ancient feature conserved from nitrogenase ancestors. We designed a paleomolecular engineering approach wherein ancestral nitrogenase genes were phylogenetically reconstructed and inserted into the genome of the diazotrophic bacterial model, Azotobacter vinelandii, enabling an integrated assessment of both in vivo functionality and purified nitrogenase biochemistry. Nitrogenase ancestors are active and robust to variable incorporation of one or more ancestral protein subunits. Further, we find that all ancestors exhibit the reversible enzymatic mechanism for dinitrogen reduction, specifically evidenced by hydrogen inhibition, which is also exhibited by extant A. vinelandii nitrogenase isozymes. Our results suggest that life may have been constrained in its sampling of protein sequence space to catalyze one of the most energetically challenging biochemical reactions in nature. The experimental framework established here is essential for probing how nitrogenase functionality has been shaped within a dynamic, cellular context to sustain a globally consequential metabolism.

Genomic Legacies of Ancient Adaptation Illuminate GC-Content Evolution in Bacteria

Bacterial evolution is characterized by strong purifying selection as well as rapid adaptive evolution in changing environments. In this context, the genomic GC content (genomic GC) varies greatly but presents some level of phylogenetic stability, making it challenging to explain based on current hypotheses. To illuminate the evolutionary mechanisms of the genomic GC, we analyzed the base composition and functional inventory of 11,083 representative genomes. A phylogenetically constrained bimodal distribution of the genomic GC, which mainly originated from parallel divergences in the early evolution, was demonstrated. Such variation of the genomic GC can be well explained by DNA replication and repair (DRR), in which multiple pathways correlate with the genomic GC. Furthermore, the biased conservation of various stress-related genes, especially the DRR-related ones, implies distinct adaptive processes in the ancestral lineages of high- or low-GC clades which are likely induced by major environmental changes. Our findings support that the mutational biases resulting from these legacies of ancient adaptation have changed the course of adaptive evolution and generated great variation in the genomic GC. This highlights the importance of indirect effects of natural selection, which indicates a new model for bacterial evolution. IMPORTANCE GC content has been shown to be an important factor in microbial ecology and evolution, and the genomic GC of bacteria can be characterized by great intergenomic heterogeneity, high intragenomic homogeneity, and strong phylogenetic inertia, as well as being associated with the environment. Current hypotheses concerning direct selection or mutational biases cannot well explain these features simultaneously. Our findings of the genomic GC showing that ancient adaptations have transformed the DRR system and that the resulting mutational biases further contributed to a bimodal distribution of it offer a more reasonable scenario for the mechanism. This would imply that, when thinking about the evolution of life, diverse processes of adaptation exist, and combined effects of natural selection should be considered.

The bio-inspired heterogeneous single-cluster catalyst Ni100-Fe4S4 for enhanced electrochemical CO2 reduction to CH4

Electrochemical conversion of CO₂-to-CH₄ is a process of converting the inert greenhouse gas into energy molecules. It offers great promise for the transformation of carbon-neutral economy. However, achieving high CH₄ activity and selectivity remains a major challenge because the electrochemical reduction of CO₂-to-CH₄ is accompanied by various C₁ intermediates at the catalytic site, involving multiple proton-coupled electron transfer processes. Herein, different from the traditional designing strategy, we propose a bio-inspired theoretical design approach to construct a heterogeneous single-cluster catalyst Ni100-Fe₄S₄ at the atomic level, which may show high CO₂ electroreduction performance. Combined with the crystallographic data and theoretical calculations, Ni100-Fe₄S₄ and CO dehydrogenase exhibit highly similar catalytic geometric active centers and CO₂ binding modes. By exploring the origin of the catalytic activity of this biomimetic structure, we found that the activation of CO₂ on Ni100-Fe₄S₄ theoretically exceeds that on natural CO dehydrogenase. Density functional theory calculations reveal that the dehydrogenase enzyme-liked Fe-Ni active site serves as an electron enrichment 'electro-bridge' (an electron-rich highly active catalytic site), which can activate CO₂ molecules efficiently and stabilize various intermediates in multistep elementary reactions to selectively produce CH₄ at a low overpotential (0.13 eV). The calculated CO₂ electroreduction pathways are well consistent with the nickel-based catalytic materials reported in experimental studies. Our work showcases and highlights the rational design of high-performance catalytic materials via the biomimetic methodology at the atomic level.

Synergies Between Venus & Exoplanetary Observations: Venus and Its Extrasolar Siblings

Here we examine how our knowledge of present day Venus can inform terrestrial exoplanetary science and how exoplanetary science can inform our study of Venus. In a superficial way the contrasts in knowledge appear stark. We have been looking at Venus for millennia and studying it via telescopic observations for centuries. Spacecraft observations began with Mariner 2 in 1962 when we confirmed that Venus was a hothouse planet, rather than the tropical paradise science fiction pictured. As long as our level of exploration and understanding of Venus remains far below that of Mars, major questions will endure. On the other hand, exoplanetary science has grown leaps and bounds since the discovery of Pegasus 51b in 1995, not too long after the golden years of Venus spacecraft missions came to an end with the Magellan Mission in 1994. Multi-million to billion dollar/euro exoplanet focused spacecraft missions such as JWST, and its successors will be flown in the coming decades. At the same time, excitement about Venus exploration is blooming again with a number of confirmed and proposed missions in the coming decades from India, Russia, Japan, the European Space Agency (ESA) and the National Aeronautics and Space Administration (NASA). Here we review what is known and what we may discover tomorrow in complementary studies of Venus and its exoplanetary cousins.

A New Ecological and Evolutionary Perspective on the Emergence of Oxygenic Photosynthesis

In this hypothesis article, we propose that the timing of the evolution of oxygenic photosynthesis and the diversification of cyanobacteria is firmly tied to the geological evolution of Earth in the Mesoarchean to Neoarchean. Specifically, the diversification of species capable of oxygenic photosynthesis is tied to the growth of subaerial (above sea-level/terrestrial) continental crust, which provided niches for their diversification. Moreover, we suggest that some formerly aerobic bacterial lineages evolved to become anoxygenic photosynthetic as a result of changes in selection following the reintroduction of ferruginous conditions in the oceans at 1.88 GYa. Both conclusions are fully compatible with phylogenetic evidence. The hypothesis carries with it a predictive component-at least for terrestrial organisms-that the development and expansion of photosynthesis species was dependent on the geological evolution of Earth.

The elements of life: A biocentric tour of the periodic table

Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.

Water oxidation in oxygenic photosynthesis studied by magnetic resonance techniques

The understanding of light-induced biological water oxidation in oxygenic photosynthesis is of great importance both for biology and (bio)technological applications. The chemically difficult multistep reaction takes place at a unique protein-bound tetra-manganese/calcium cluster in photosystem II whose structure has been elucidated by X-ray crystallography (Umena et al. Nature 2011, 473, 55). The cluster moves through several intermediate states in the catalytic cycle. A detailed understanding of these intermediates requires information about the spatial and electronic structure of the Mn₄ Ca complex; the latter is only available from spectroscopic techniques. Here, the important role of Electron Paramagnetic Resonance (EPR) and related double resonance techniques (ENDOR, EDNMR), complemented by quantum chemical calculations, is described. This has led to the elucidation of the cluster's redox and protonation states, the valence and spin states of the manganese ions and the interactions between them, and contributed substantially to the understanding of the role of the protein surrounding, as well as the binding and processing of the substrate water molecules, the O-O bond formation and dioxygen release. Based on these data, models for the water oxidation cycle are developed.