Early Earth Research Articles

Cysteine‐Based Dynamic Self‐Assembly and Their Importance in the Origins of Life

The knowledge regarding the origin of life from inanimate materials is still elusive. It was proposed that biological building blocks evolved from the inorganic substances in the early earth conditions. However, the process by which chemistry can be converted into biology has not yet been achieved in the laboratory. The artificial system in the out‐of‐equilibrium state must maintain a few critical features of life, like compartmentalization, metabolism, and replication, to be considered alive. In this direction, working with cysteine (Cys)‐based molecules is strategic to understand the life evolution process. The presence of the sulphydryl (‐SH) group in the Cys‐residue can build a dynamic equilibrium state through disulfide redox chemistry under the proper guidance of oxidizing and reducing agents. In this review article, our primary focus is to discuss the Cys‐containing short‐peptide‐based self‐assembly and disassembly processes. The formation of disulfide bonds sometimes helps in the self‐assembly process and gelation, but the reverse is also true in some cases. In the later part of this article, we cover the fact that these sulphydryl‐based systems have shown their adaptability to mimic different life‐essential criteria to participate in Darwinian evolution.

Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts

Geothermal springs house unicellular red algae in the class Cyanidiophyceae that dominate the microbial biomass at these sites. Little is known about host-virus interactions in these environments. We analyzed the virus community associated with red algal mats in three neighboring habitats (creek, endolithic, soil) at Lemonade Creek, Yellowstone National Park (YNP), USA. We find that despite proximity, each habitat houses a unique collection of viruses, with the giant viruses, Megaviricetes, dominant in all three. The early branching phylogenetic position of genes encoded on metagenome assembled virus genomes (vMAGs) suggests that the YNP lineages are of ancient origin and not due to multiple invasions from mesophilic habitats. The existence of genomic footprints of adaptation to thermophily in the vMAGs is consistent with this idea. The Cyanidiophyceae at geothermal sites originated ca. 1.5 Bya and are therefore relevant to understanding biotic interactions on the early Earth.

Methanogen‐Mediated Precipitation of Mn Carbonates at the Expense of Mn Oxides

AbstractWhether Mn carbonates can be used as a proxy for the oxygenation event is debated. Here we examined the Early Cretaceous lacustrine Mn carbonates from North China, which contain abundant microbial fossils. The extremely positive δ13C (up to +15‰ relative to Vienna Peedee belemnite) and micro‐area enrichment of Ni strongly indicate a methanogenic archaea origin of these microorganisms. Transmission electron microscope and electron energy loss spectroscopy show the nanoscale transformation of Mn‐oxides (Mg‐exchanged phyllomanganate) to Mn carbonates (kutnohorite), on extracellular polymeric substances. The reaction of the Mn oxides with organic matter resulted in increasing pH and alkalinity, together with the fluctuating pH, offering a suitable micro‐environment for the transformation processes. These Mn carbonates are therefore indicative of an oxidized, sulfate‐absent environment. The depicted scenario serves as a reference to ocean of the early Earth and provides a referable Mn oxide tracer for determining the emergence of the Great Oxidation Event.

Visualizing ribonuclease digestion of RNA-like polymers produced by hot wet-dry cycles

Polymerization of nucleotides under prebiotic conditions simulating the early Earth has been extensively studied. Several independent methods have been used to verify that RNA-like polymers can be produced by hot wet-dry cycling of nucleotides. However, it has not been shown that these RNA-like polymers are similar to biological RNA with 3’-5’ phosphodiester bonds. In the results described here, RNA-like polymers were generated from 5’-monophosphate nucleosides AMP and UMP. To confirm that the polymers resemble biological RNA, ribonuclease A should catalyze hydrolysis of the 3’-5’ phosphodiester bonds between pyrimidine nucleotides to each other or to purine nucleotides, but not purine-purine nucleotide bonds. Here we show AFM images of specific polymers produced by hot wet-dry cycling of AMP, UMP and AMP/UMP (1:1) solutions on mica surfaces, before and after exposure to ribonuclease A. AMP polymers were unaffected by ribonuclease A but UMP polymers disappeared. This indicates that a major fraction of the bonds in the UMP polymers is indeed 3’-5’ phosphodiester bonds. Some of the polymers generated from the AMP/UMP mixture also showed clear signs of cleavage. Because ribonuclease A recognizes the ester bonds in the polymers, we show for the first time that these prebiotically produced polymers are in fact similar to biological RNA but are likely to be linked by a mixture of 3’-5’ and 2’-5’ phosphodiester bonds.

Sequestration of helium and xenon via iron-halide compounds in early Earth

The terrestrial abundance anomalies of helium and xenon suggest the presence of deep-Earth reservoirs of these elements, which has led to great interest in searching for materials that can host these usually unreactive elements. Here, using an advanced crystal structure search approach in conjunction with first-principles calculations, we show that several Xe/He-bearing iron halides are thermodynamically stable in a broad region of P–T phase space below 60 GPa. Our results present a compelling case for sequestration of He and Xe in the early Earth and may suggest their much wider distribution in the present Earth than previously believed. These findings offer insights into key material-based and physical mechanisms for elucidating major geological phenomena.

RETRACTED: Sturtz, M.; House, C. Metal Catalysis Acting on Nitriles in Early Earth Hydrothermal Systems. Life 2023, 13, 1524

The Life Editorial Office retracts the article, “Metal Catalysis Acting on Nitriles in Early Earth Hydrothermal Systems” [...]

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.

The Lanseria palaeosol: Implications for palaeoweathering and terrestrial life at ∼2.6 Ga on the Kaapvaal Craton

Archaean palaeosols are a rare record of surface processes on the early Earth. We report on the discovery of a palaeoweathering profile developed at the contact between Mesoarchaean basement and the Neoarchaean to Palaeoproterozoic Transvaal Supergroup along the northern margin of the Johannesburg Dome, Kaapvaal Craton. Granodiorite ∼3.1 Ga old was subjected to weathering just prior to the deposition of the ∼2.6 Ga Black Reef Formation. The ∼25 m-thick profile is dominated by a palaeosaprolite and organic matter-rich palaeosol remnant at the top that experienced erosion upon marine transgression on the Kaapvaal Craton. The Al concentration of the profile, sericite content and chemical index of alteration (CIA) values progressively increase from the parent granodiorite towards the nonconformity as Fe, Mg, Na and Ca concentrations decrease. The decrease of Co and Zn together with Fe and the retention of U, V and Cr collectively suggest a reducing and acidic environment at the time of weathering. Carbonaceous matter with negative δ13C isotopic values (−27 to −23 ‰V-PDB) in the palaeosol is compatible with the former presence of photoautotrophic microbes. Copper depletion and mobility of P may indicate the presence of organic acids that enhanced chemical weathering of the bedrock. The palaeoweathering profile was subjected to diagenetic-hydrothermal K-metasomatism, regional metamorphism and deformation, which collectively transformed the regolith into a quartz-sericite schist, as it presently occurs. Despite these modifications, the original record of palaeoweathering and microbial colonisation is well preserved. Colonisation of a large swath of the Kaapvaal Craton by terrestrial soil-dwelling microbiota at 2.60 Ga is recorded in abundant soil-derived carbonaceous matter in transgressive marine conglomerates that erosively overlie the palaeosol.

High-Fidelity RNA Copying via 2',3'-Cyclic Phosphate Ligation.

Templated ligation offers an efficient approach to replicate long strands in an RNA world. The 2',3'-cyclic phosphate (>P) is a prebiotically available activation that also forms during RNA hydrolysis. Using gel electrophoresis and high-performance liquid chromatography, we found that the templated ligation of RNA with >P proceeds in simple low-salt aqueous solutions with 1 mM MgCl2 under alkaline pH ranging from 9 to 11 and temperatures from -20 to 25 °C. No additional catalysts were required. In contrast to previous reports, we found an increase in the number of canonical linkages to 50%. The reaction proceeds in a sequence-specific manner, with an experimentally determined ligation fidelity of 82% at the 3' end and 91% at the 5' end of the ligation site. With splinted oligomers, five ligations created a 96-mer strand, demonstrating a pathway for the ribozyme assembly. Due to the low salt requirements, the ligation conditions will be compatible with strand separation. Templated ligation mediated by 2',3'-cyclic phosphate in alkaline conditions therefore offers a performant replication and elongation reaction for RNA on early Earth.

Organic matter accumulation as a convergence response to astronomical forcing: Insights from Milankovitch periods and sea-level fluctuations during the early Cambrian

The accumulation of organic matter (OM) in marine sediments is a vital part of the global carbon cycle today and on ancient Earth, and is driven by a cumulative shift of organic carbon flux through oceans to marine sediments. This shift is a complicated process that is known to be influenced by the biological pump, diagenesis, and thermal alteration, so is affected by oceanic conditions and palaeo-climate, but less attention has been paid to the triggers of OM accumulation. Here, a set of marine sedimentary rocks from the early Cambrian in the southwestern part of the Yangtze Platform in China was used to search for clues to the triggers of OM accumulation. The effect of astronomical forcing, which potentially is a major control on Earth's oceanic conditions, was assessed via frequency analysis based on a high-resolution log dataset from a borehole in Yunnan Province. An astronomical time scale was constructed based on a 405,000 year-tuned filter. Palaeo-oceanic sedimentary conditions and palaeo-climate, which were recorded in the sedimentary rocks, were determined through geochemical analyses of major, trace, and rare earth elements. The mutual influence of astronomical forcing and the early Earth oceanic sedimentary conditions and paleoclimate were examined though Pearson Correlation analyses to provide evidence for the intensity of alteration of sedimentary conditions and the forces impacting the shift of organic carbon in the marine ecosystem. The results show that two convergence responses of OM accumulation were associated with ca. 1.5 and 2.4 million year (Myr) Milankovitch cycles. Fluctuations in sea level establish a connection between Milankovitch forcings and changes in sedimentary conditions, thereby providing evidence for the triggering of a cumulative shift of OM flux to sediments, and the effect of astronomical forcing on the organic carbon cycle.

The value of the Belingwe Greenstone Belt, Zimbabwe, as a national Geoheritage site

Abstract Products of geological processes such as rock formations, unconformities, structures, minerals, fossils, and landforms, represent unique records of the evolution of the Earth. These form a coherent picture showing how the Earth evolved. The picture becomes blurred with antiquity. Consequently, there are challenges in gathering information from the Archaean, the period during which the foundations of the Earth were laid down. The 2.7 Ga Belingwe Greenstone Belt in Zimbabwe has proved to be valuable because it has some of the best-preserved Archaean stratigraphy in the world. An unconformity between sialic basement and supracrustal rocks of the greenstone belt, and exotic rocks such as komatiites and stromatolites, are immensely contributing towards the knowledge about the evolution of the young Earth and the beginning of life. The frequent use of the Belingwe Greenstone Belt examples to explain geotectonic processes of the early Earth give testimony to the importance of this structure. Interpretation of some of the features of the greenstone belt is sometimes controversial, which forms areas of endless research to better understand the Archaean Era. It is for these reasons that arguments are presented for consideration of the Belingwe Greenstone Belt as a national Geoheritage site.

Modelling energy-harvesting processes in primitive cells: Proton transport across bilayers driven by the oxidation of sulfite

A frequently debated topic related to the origin of life centers around the question of how complex forms of life on today's Earth may have evolved over time from simpler predecessors. For example, the question of how proton concentration gradients across cellular membranes developed in ancestral protocells remains unanswered. This process, which is indispensable for the generation of chemical energy in modern organisms, is driven by energy derived from redox processes in the respiratory chain. Since it is highly unlikely that the complex machinery of the respiratory chain was available on early Earth, we provide an example of how proton gradients can be established in less complex systems. Utilizing liposomes as models of primitive cells, we were able to generate proton gradients of about two pH units across the liposome bilayers using redox reactions as the driving force. Electrons were transferred from sodium sulfite present on the outside of the liposomes to ferricyanide, which was trapped on the inside. A lipid-soluble phenazine derivative served as a shuttle that transferred both electrons and protons across the lipid bilayer. Because sulfite would have been an abundant reduced solute available to the earliest cells, we propose that it may have been a primary source of redox energy for primitive chemiosmotic energy transduction.

A Prebiotic Precursor to Life's Phosphate Transfer System with an ATP Analog and Histidyl Peptide Organocatalysts.

Biochemistry is dependent upon enzyme catalysts accelerating key reactions. At the origin of life, prebiotic chemistry must have incorporated catalytic reactions. While this would have yielded much needed amplification of certain reaction products, it would come at the possible cost of rapidly depleting the high energy molecules that acted as chemical fuels. Biochemistry solves this problem by combining kinetically stable and thermodynamically activated molecules (e.g., ATP) with enzyme catalysts. Here, we demonstrate a prebiotic phosphate transfer system involving an ATP analog (imidazole phosphate) and histidyl peptides, which function as organocatalytic enzyme analogs. We demonstrate that histidyl peptides catalyze phosphorylations via a phosphorylated histidyl intermediate. We integrate these histidyl-catalyzed phosphorylations into a complete prebiotic scenario whereby inorganic phosphate is incorporated into organic compounds though physicochemical wet-dry cycles. Our work demonstrates a plausible system for the catalyzed production of phosphorylated compounds on the early Earth and how organocatalytic peptides, as enzyme precursors, could have played an important role in this.

Cation exchange to montmorillonite induces selective adsorption of amino acids

Concentrating simple organic molecules, such as amino acids, in the adsorbed phase could have been an early step in prebiotic evolution towards more complex bio-macromolecules on the early Earth. Smectite clay minerals represent potential selective sorbents for prebiotic molecules because of their negative structural charge and high surface area. This study evaluated the adsorption behavior of amino acids to montmorillonite, a well-characterized smectite, at varying pH and fluid compositions. At both pH 5 and 7 in a sodium chloride fluid, amino acids with basic sidechains (L-arginine and L-lysine), which are primarily cationic under these conditions, were selectively adsorbed to montmorillonite with Langmuir constants much greater than amino acids that were predominantly zwitterionic or anionic in solution. On average, the Langmuir constants for the cationic amino acids were 30 (pH 5) and 50 (pH 7) times greater than the constants for zwitterionic amino acids and 120 (pH 5) and 80 (pH 7) times greater than the constants for L-glutamic acid. Under the same pH conditions in a magnesium chloride solution, the adsorption of L-arginine and L-lysine was substantially inhibited with Langmuir constants ∼ 10 times smaller. These observations suggest that cation exchange is the dominant adsorption mechanism for amino acids on montmorillonite. X-ray diffraction and infrared spectroscopy indicate that L-arginine and L-lysine enter the smectite interlayer where the protonated amino sidechain has the strongest interactions with the mineral surface, further supporting adsorption driven primarily through electrostatic interactions. Therefore, smectites on the early Earth may have selectively concentrated cationic amino acids, providing a potential template for the polymerization of α-amine linked peptides.

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.

Paired Si-O isotopes decipher the onset of supracrustal recycling in the early Earth

The Precambrian continental record: a window into early Earth environments

The Precambrian was characterized by unique palaeoenvironmental conditions in the Earth’s atmosphere, biosphere and geosphere. This study presents a global quantitative analysis of sedimentary successions associated with aeolian, alluvial, fluvial, lacustrine and glacigenic depositional systems of Precambrian age, examined in the broader context of Earth evolution. In the Precambrian, an apparent scarcity of aeolian successions is observed. This may be linked to: (i) differences in atmospheric density, which controlled wind erosion and sedimentation; (ii) different astronomical configurations, which may have influenced tides and atmospheric circulation, thereby affecting sand availability and the width of subtropical zones; (iii) potentially hotter and more humid climates, restricting dry-sand availability; (iv) a lack of vascular vegetation that could prevent reworking of aeolian deposits; (v) poor preservation potential; (vi) misinterpretation of the Precambrian record. Mixed aeolian-alluvial strata are more abundant, perhaps because their preservation in the geological record was favoured by water-tables sustained by incursions of alluvial systems into otherwise aeolian dominated environments. Aeolian deposits were preferentially accumulated during phases of supercontinental breakup, where rapidly subsiding rift basins provided accommodation suitable for preservation. Other than in the Neoproterozoic record, where glacigenic deposits dominate, alluvial strata are the most common and thickest type of continental deposit in the Precambrian. Precambrian braided alluvial systems were more widespread than in the Phanerozoic. Major alluvial systems formed preferentially during phases of supercontinent assembly, whereby alluvial systems drained major orogens, and long drainage pathways developed from supercontinent interiors to coastlines. In the Paleoproterozoic, ephemeral, saline to partly arid lakes developed extensively in the desertic interior of Columbia. Glacial deposits preferentially formed in the breakup phase of supercontinental cycles; this supports theories invoking enhanced chemical weathering of uplifted rift shoulders as a driver of carbon dioxide sequestration, global cooling, and glaciation. Overall, the number of identified continental successions increases towards the Precambrian-Phanerozoic boundary. This may be an artefact of an increasingly more complete stratigraphic record as time progresses. However, the abundance of continental successions varies on a quasi-periodic cycle of 500 – 700 Myr, with peaks coinciding with the tenure and breakup of Precambrian supercontinents.

Magnesium silicate chimneys at the Strytan hydrothermal field, Iceland, as analogues for prebiotic chemistry at alkaline submarine hydrothermal vents on the early Earth

The Strytan Hydrothermal Field (SHF) in basaltic terrain in Iceland is one of the extant alkaline submarine hydrothermal vent systems favoured as analogues for where life on Earth may have begun. To test this hypothesis we analyse the composition, structure, and mineralogy of samples from hydrothermal chimneys generated at the SHF. We find that the chimney precipitates are composed of Mg-silicates including clays of the saponite-stevensite group (high Mg and Si, low Fe and Al), Ca-carbonates and Ca-sulfates. The chimneys comprise permeable structures with pores sizes down to 1 µm or less. Their complex interiors as observed with SEM (Scanning Electron Microscopy) and X-ray CT (computed tomography scanning), exhibit high internal surface areas. EDX (energy-dispersive X-ray spectroscopy) analysis reveals an increase in the Mg/Si ratio toward the chimney exteriors. Chemical garden analogue experiments produce similar Mg–silicate chimneys with porous internal structures, indicating that injection-precipitation experiments can be high-fidelity analogues for natural hydrothermal chimneys at the SHF. We conclude that SHF chimneys could have facilitated prebiotic reactions comparable to those proposed for clays and silica gels at putative Hadean to Eoarchean alkaline vents. Analysis of the fluid dynamics shows that these chimneys are intermediate in growth rate compared to faster black smokers though slower than those at Lost City. The SHF is proposed as a prebiotic alkaline vent analogue for basaltic terrains on the early Earth.

LATE ARCHEAN SHELF-TO-BASIN IRON SHUTTLE CONTRIBUTES TO THE FORMATION OF THE WORLD-CLASS DATAIGOU BANDED IRON FORMATION

Abstract Banded iron formations (BIFs) are among the few chemical sedimentary archives that capture the biogeochemical evolution of Fe cycling and the redox evolution of the early Earth. Although biologically recycled continental Fe has been previously proposed to be a significant source of Fe in BIFs deposited from a stratified ocean at the onset of the Great Oxidation Event (GOE; ~2.5–2.2 Ga), constraining Fe sources and pathways in Archean BIFs remains challenging. Here we present major and trace element and Fe-Nd-Cr isotope data for the largest BIF (i.e., Dataigou) in China to test whether a benthic Fe shuttle was operative during deposition of pre-GOE BIFs. The absence of true, shale-normalized Ce anomalies, coupled with unfractionated Cr and positive Fe isotope compositions, suggests that BIF deposition occurred in an anoxic water column under reducing atmospheric conditions, whereas positive Eu anomalies indicate a significant input from a high-temperature hydrothermal source. Based on a significant correlation between initial Nd and Fe isotope data, we suggest that two Fe sources were periodically mixed and resulted in deposition of the Dataigou BIF. Here, we suggest the following sources: (1) hydrothermal fluids from sea-floor systems (low εNd(t) and high δ56Fe), derived from the interaction of fluids with underlying, older continental crust, and (2) a benthic Fe flux (high εNd(t) and low δ56Fe), generated by microbial Fe(III) reduction in coastal sediments during weathering of a nearby depleted landmass. Results presented here confirm, for the first time, that a microbially driven Fe shuttle was operational and supplied Fe on a basin-wide scale in the absence of atmospheric oxygen.

Prebiotically plausible chemoselective pantetheine synthesis in water.

Coenzyme A (CoA) is essential to all life on Earth, and its functional subunit, pantetheine, is important in many origin-of-life scenarios, but how pantetheine emerged on the early Earth remains a mystery. Earlier attempts to selectively synthesize pantetheine failed, leading to suggestions that "simpler" thiols must have preceded pantetheine at the origin of life. In this work, we report high-yielding and selective prebiotic syntheses of pantetheine in water. Chemoselective multicomponent aldol, iminolactone, and aminonitrile reactions delivered spontaneous differentiation of pantoic acid and proteinogenic amino acid syntheses, as well as the dihydroxyl, gem-dimethyl, and β-alanine-amide moieties of pantetheine in dilute water. Our results are consistent with a role for canonical pantetheine at the outset of life on Earth.