The Archean sulfur cycle and the early history of atmospheric oxygen

Sulfur isotope analyses using 3× elemental analysis/isotope ratio mass spectrometry: Saving helium and energy while reducing analytical time and costs

RATIONALE

Helium (He) and energy shortages have caused price increases and reduced their availability. Using three combustion reactions per acquisition of carbon and nitrogen isotope ratios saves 50% He and energy during the elemental analysis/isotope ratio mass spectrometry (EA/IRMS). This approach needs to be tested for sulfur isotope (δ34S) analyses.

METHODS

A new method to measure δ34S in three sequential combustion reactions within one EA/IRMS acquisition was developed. The same material or blank samples could be used in the three reactions. After SO2 was used, a N2 purging method was employed to prolong the lifetime of the valves in the EA/IRMS interface. The 3×EA/IRMS was applied to measure δ34S in precious samples, such as Ag2S from acid-volatile and chromium-reducible sulfur extracted with a multiple-port setup.

RESULTS

The 3×EA/IRMS-δ34S method was validated with replicate analyses of international reference materials and laboratory standards with a wide range of mineralogical compositions and δ34S values. The method provided a strategic advantage for the δ34S measurements of small precious samples (measured between blanks). The accuracy and precision of the 3×EA/IRMS values effectively matched those obtained using conventional EA/IRMS, with good agreement between the mean ± SD values and the recommended values with their uncertainties.

CONCLUSIONS

Compared with the conventional EA/IRMS, the proposed method provides accurate and precise δ34S measurements of the sulfate and sulfide samples while saving approximately 50% of He, energy, SO2 reference gas, O2, analysis time, and cost. Notably, 3×EA/IRMS can provide up to three δ34S values unaffected by memory effects.

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.

Abiotic formation of alkylsulfonic acids in interstellar analog ices and implications for their detection on Ryugu

For the last century, the source of sulfur in Earth's very first organisms has remained a fundamental, unsolved enigma. While sulfates and their organic derivatives with sulfur in the S(+VI) oxidation state represent core nutrients in contemporary biochemistry, the limited bioavailability of sulfates during Earth's early Archean period proposed that more soluble S(+IV) compounds served as the initial source of sulfur for the first terrestrial microorganisms. Here, we reveal via laboratory simulation experiments that the three simplest alkylsulfonic acids-water soluble organic S(+IV) compounds-can be efficiently produced in interstellar, sulfur-doped ices through interaction with galactic cosmic rays. This discovery opens a previously elusive path into the synthesis of vital astrobiological significance and untangles fundamental mechanisms of a facile preparation of sulfur-containing, biorelevant organics in extraterrestrial ices; these molecules can be eventually incorporated into comets and asteroids before their delivery and detection on Earth such as in the Murchison, Tagish Lake, and Allende meteorites along with the carbonaceous asteroid Ryugu.

Hexose phosphorylation for a non-enzymatic glycolysis and pentose phosphate pathway on early Earth

Glycolysis and pentose phosphate pathways play essential roles in cellular processes and are assumed to be among the most ancient metabolic pathways. Non-enzymatic metabolism-like reactions might have occurred on the prebiotic Earth and been inherited by the biological reactions. Previous research has identified a part of the non-enzymatic glycolysis and the non-enzymatic pentose phosphate pathway from glucose 6-phosphate and 6-phosphogluconate, which are intermediates of these reactions. However, how these phosphorylated molecules were formed on the prebiotic Earth remains unclear. Herein, we demonstrate the synthesis of glucose and gluconate from simple aldehydes in alkaline solutions and the formation of glucose 6-phosphate and 6-phosphogluconate with borate using thermal evaporation. These results imply that the initial stages of glycolysis-like and pentose phosphate pathway-like reactions were achieved in borate-rich evaporative environments on prebiotic Earth, suggesting that non-enzymatic metabolism provided biomolecules and their precursors on prebiotic Earth.

Fossilized giant sulfide-oxidizing bacteria from the Devonian Hollard Mound seep deposit, Morocco

The giant sulfide-oxidizing bacteria are particularly prone to preservation in the rock record, and their fossils have been identified in ancient phosphorites, cherts, and carbonates. This study reports putative spherical fossils preserved in the Devonian Hollard Mound hydrocarbon-seep deposit. Based on petrographical, mineralogical, and geochemical evidence the putative microfossils are interpreted as sulfide-oxidizing bacteria similar to the present-day genus Thiomargarita, which is also found at modern hydrocarbon seeps. The morphology, distribution, size, and occurrence of the fossilized cells show a large degree of similarity to their modern counterparts. Some of the spherical fossils adhere to worm tubes analogous to the occurrence of modern Thiomargarita on the tubes of seep-dwelling siboglinid worms. Fluorapatite crystals were identified within the fossilized cell walls, suggesting the intercellular storage of phosphorus analogous to modern Thiomargarita cells. The preservation of large sulfide-oxidizing bacteria was probably linked to changing biogeochemical processes at the Hollard Mound seep or, alternatively, may have been favored by the sulfide-oxidizing bacteria performing nitrate-dependent sulfide oxidation-a process known to induce carbonate precipitation. The presence of sulfide-oxidizing bacteria at a Devonian hydrocarbon seep highlights the similarities of past and present chemosynthesis-based ecosystems and provides valuable insight into the antiquity of biogeochemical processes and element cycling at Phanerozoic seeps.

Are Large Sulfur Isotope Variations Biosignatures in an Ancient, Impact-Induced Hydrothermal Mars Analog?

Discrepancies have emerged concerning the application of sulfur stable isotope ratios as a biosignature in impact crater paleolakes. The first in situ δ34S data from Mars at Gale crater display a ∼75‰ range that has been attributed to an abiotic mechanism. Yet biogeochemical studies of ancient environments on Earth generally interpret δ34S fractionations >21‰ as indicative of a biological origin, and studies of δ34S at analog impact crater lakes on Earth have followed the same approach. We performed analyses (including δ34S, total organic carbon wt%, and scanning electron microscope imaging) on multiple lithologies from the Nördlinger Ries impact crater, focusing on hydrothermally altered impact breccias and associated sedimentary lake-fill sequences to determine whether the δ34S properties define a biosignature. The differences in δ34S between the host lithologies may have resulted from thermochemical sulfate reduction, microbial sulfate reduction, hydrothermal equilibrium fractionation, or any combination thereof. Despite abundant samples and instrumental precision currently exclusive to Earth-bound analyses, assertions of biogenicity from δ34S variations >21‰ at the Miocene Ries impact crater are tenuous. This discourages the use of δ34S as a biosignature in similar environments without independent checks that include the full geologic, biogeochemical, and textural context, as well as a comprehensive acknowledgment of alternative hypotheses.

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.

Isotopic history of seawater: the stable isotope character of the global ocean at present and in the geological past

After the atmosphere, the ocean is the most well-mixed and homogeneous global geochemical reservoir. Both physical and biological processes generate elemental and isotope variations in seawater. Contrasting geochemical behaviors cause elements to be susceptible to different fractionation mechanisms, with their isotopes providing unique insights into the composition and evolution of the ocean over the course of geological history. Supplementing the traditional stable isotopes (H, C, O, N, S) that provide information about ocean processes and past environmental conditions, radiogenic isotope (Sr, Nd, Os, Pb, U) systems can be used as time markers, indicators of terrestrial weathering, and ocean water mass mixing. Recent instrumentation advances have made possible the measurement of natural stable isotope variations produced by both mass-dependent and mass-independent fractionation for an ever-increasing number of metal elements (e.g. Li, B, Mg, Si, Ca, V, Cr, Fe, Ni, Cu, Zn, Se, Mo, Cd, Tl, U). The major emphasis in this review is on the isotopic composition of the light elements based on a comparatively large literature. Unlike O, H and S, the stable isotopes of C, N and Si do not have a constant isotopic composition in the modern ocean. The major cations Ca, Mg, and Sr fixed in carbonate shells provide the best proxies for reconstruction of the composition of the ocean in the past. Exhibiting large isotope enrichments in ocean water, B and Li are suitable for the investigation of water/rock interactions and can act as monitors of former oceanic pH. The bioessential elements Zn, Cd, and Ni are indicators of paleoproductivity in the ocean. Characteristic isotope enrichments or depletions of the multivalent elements V, Cr, Fe, Se, Mo, and U record the past redox state of the ocean/atmosphere system. Case studies describe how isotopes have been used to define the seawater composition in the geological past.

Cell-specific rates of sulfate reduction and fermentation in the sub-seafloor biosphere

Microorganisms in subsurface sediments live from recalcitrant organic matter deposited thousands or millions of years ago. Their catabolic activities are low, but the deep biosphere is of global importance due to its volume. The stability of deeply buried sediments provides a natural laboratory where prokaryotic communities that live in steady state with their environments can be studied over long time scales. We tested if a balance is established between the flow of energy, the microbial community size, and the basal power requirement needed to maintain cells in sediments buried meters below the sea floor. We measured rates of carbon oxidation by sulfate reduction and counted the microbial cells throughout ten carefully selected sediment cores with ages from years to millions of years. The rates of carbon oxidation were converted to power (J s-1 i.e., Watt) using the Gibbs free energy of the anaerobic oxidation of complex organic carbon. We separated energy dissipation by fermentation from sulfate reduction. Similarly, we separated the community into sulfate reducers and non-sulfate reducers based on the dsrB gene, so that sulfate reduction could be related to sulfate reducers. We found that the per-cell sulfate reduction rate was stable near 10-2 fmol C cell-1 day-1 right below the zone of bioturbation and did not decrease with increasing depth and sediment age. The corresponding power dissipation rate was 10-17 W sulfate-reducing cell-1. The cell-specific power dissipation of sulfate reducers in old sediments was similar to the slowest growing anaerobic cultures. The energy from mineralization of organic matter that was not dissipated by sulfate reduction was distributed evenly to all cells that did not possess the dsrB gene, i.e., cells operationally defined as fermenting. In contrast to sulfate reducers, the fermenting cells had decreasing catabolism as the sediment aged. A vast difference in power requirement between fermenters and sulfate reducers caused the microbial community in old sediments to consist of a minute fraction of sulfate reducers and a vast majority of fermenters.

Sulfate triple-oxygen-isotope evidence confirming oceanic oxygenation 570 million years ago

The largest negative inorganic carbon isotope excursion in Earth's history, namely the Ediacaran Shuram Excursion (SE), closely followed by early animal radiation, has been widely interpreted as a consequence of oceanic oxidation. However, the primary nature of the signature, source of oxidants, and tempo of the event remain contested. Here, we show that carbonate-associated sulfate (CAS) from three different paleocontinents all have conspicuous negative ¹⁷O anomalies (Δ'¹⁷O_CAS values down to -0.53‰) during the SE. Furthermore, the Δ'¹⁷O_CAS varies in correlation with its corresponding δ³⁴S_CAS and δ¹⁸O_CAS as well as the carbonate δ¹³C_carb, decreasing initially followed by a recovery over the ~7-Myr SE duration. In a box-model examination, we argue for a period of sustained water-column ventilation and consequently enhanced sulfur oxidation in the SE ocean. Our findings reveal a direct involvement of mass-anomalously ¹⁷O-depleted atmospheric O₂ in marine sulfate formation and thus a primary global oceanic oxygenation event during the SE.

Metals in Prebiotic Catalysis: A Possible Evolutionary Pathway for the Emergence of Metalloproteins

Proteinaceous catalysts found in extant biology are products of life that were potentially derived through prolonged periods of evolution. Given their complexity, it is reasonable to assume that they were not accessible to prebiotic chemistry as such. Nevertheless, the dependence of many enzymes on metal ions or metal-ligand cores suggests that catalysis relevant to biology could also be possible with just the metal centers. Given their availability on the Hadean/Archean Earth, it is fair to conjecture that metal ions could have constituted the first forms of catalysts. A slow increase of complexity that was facilitated through the provision of organic ligands and amino acids/peptides possibly allowed for further evolution and diversification, eventually demarcating them into specific functions. Herein, we summarize some key experimental developments and observations that support the possible roles of metal catalysts in shaping the origins of life. Further, we also discuss how they could have evolved into modern-day enzymes, with some suggestions for what could be the imminent next steps that researchers can pursue, to delineate the putative sequence of catalyst evolution during the early stages of life.

Structures of the sulfite detoxifying F420-dependent enzyme from Methanococcales

Methanogenic archaea are main actors in the carbon cycle but are sensitive to reactive sulfite. Some methanogens use a sulfite detoxification system that combines an F₄₂₀H₂-oxidase with a sulfite reductase, both of which are proposed precursors of modern enzymes. Here, we present snapshots of this coupled system, named coenzyme F₄₂₀-dependent sulfite reductase (Group I Fsr), obtained from two marine methanogens. Fsr organizes as a homotetramer, harboring an intertwined six-[4Fe-4S] cluster relay characterized by spectroscopy. The wire, spanning 5.4 nm, electronically connects the flavin to the siroheme center. Despite a structural architecture similar to dissimilatory sulfite reductases, Fsr shows a siroheme coordination and a reaction mechanism identical to assimilatory sulfite reductases. Accordingly, the reaction of Fsr is unidirectional, reducing sulfite or nitrite with F₄₂₀H₂. Our results provide structural insights into this unique fusion, in which a primitive sulfite reductase turns a poison into an elementary block of life.

Rapid timescale for an oxic transition during the Great Oxidation Event and the instability of low atmospheric O2

Understanding the rise of atmospheric oxygen on Earth is important for assessing precursors to complex life and for evaluating potential future detections of oxygen on exoplanets as signs of extraterrestrial biospheres. However, it is unclear whether Earth’s initial rise of O₂ was monotonic or oscillatory, and geologic evidence poorly constrains O₂ afterward, during the mid-Proterozoic (1.8 billion to 0.8 billion years ago). Here, we used a time-dependent photochemical model to simulate oxygen’s rise and the stability of subsequent O₂ levels to perturbations in supply and loss. Results show that large oxygen fluctuations are possible during the initial rise of O₂ and that Mesoproterozoic O₂ had to exceed 0.01% volume concentration for atmospheric stability.

The Great Oxidation Event (GOE), arguably the most important event to occur on Earth since the origin of life, marks the time when an oxygen-rich atmosphere first appeared. However, it is not known whether the change was abrupt and permanent or fitful and drawn out over tens or hundreds of millions of years. Here, we developed a one-dimensional time-dependent photochemical model to resolve time-dependent behavior of the chemically unstable transitional atmosphere as it responded to changes in biogenic forcing. When forced with step-wise changes in biogenic fluxes, transitions between anoxic and oxic atmospheres take between only 10² and 10⁵ y. Results also suggest that O₂ between ~10−8 and ~10−4 mixing ratio is unstable to plausible atmospheric perturbations. For example, when atmospheres with these O₂ concentrations experience fractional variations in the surface CH₄ flux comparable to those caused by modern Milankovich cycling, oxygen fluctuates between anoxic (~10−8) and oxic (~10−4) mixing ratios. Overall, our simulations are consistent with possible geologic evidence of unstable atmospheric O₂, after initial oxygenation, which could occasionally collapse from changes in biospheric or volcanic fluxes. Additionally, modeling favors mid-Proterozoic O₂ exceeding 10−4 to 10−3 mixing ratio; otherwise, O₂ would periodically fall below 10−7 mixing ratio, which would be inconsistent with post-GOE absence of sulfur isotope mass-independent fractionation.

Structural evolution of the ancient enzyme, dissimilatory sulfite reductase

Dissimilatory sulfite reductase is an ancient enzyme that has linked the global sulfur and carbon biogeochemical cycles since at least 3.47 Gya. While much has been learned about the phylogenetic distribution and diversity of DsrAB across environmental gradients, far less is known about the structural changes that occurred to maintain DsrAB function as the enzyme accompanied diversification of sulfate/sulfite reducing organisms (SRO) into new environments. Analyses of available crystal structures of DsrAB from Archaeoglobus fulgidus and Desulfovibrio vulgaris, representing early and late evolving lineages, respectively, show that certain features of DsrAB are structurally conserved, including active siro-heme binding motifs. Whether such structural features are conserved among DsrAB recovered from varied environments, including hot spring environments that host representatives of the earliest evolving SRO lineage (e.g., MV2-Eury), is not known. To begin to overcome these gaps in our understanding of the evolution of DsrAB, structural models from MV2.Eury were generated and evolutionary sequence co-variance analyses were conducted on a curated DsrAB database. Phylogenetically diverse DsrAB harbor many conserved functional residues including those that ligate active siro-heme(s). However, evolutionary co-variance analysis of monomeric DsrAB subunits revealed several False Positive Evolutionary Couplings (FPEC) that correspond to residues that have co-evolved despite being too spatially distant in the monomeric structure to allow for direct contact. One set of FPECs corresponds to residues that form a structural path between the two active siro-heme moieties across the interface between heterodimers, suggesting the potential for allostery or electron transfer within the enzyme complex. Other FPECs correspond to structural loops and gaps that may have been selected to stabilize enzyme function in different environments. These structural bioinformatics results suggest that DsrAB has maintained allosteric communication pathways between subunits as SRO diversified into new environments. The observations outlined here provide a framework for future biochemical and structural analyses of DsrAB to examine potential allosteric control of this enzyme.

Microbial Diversity and Sulfur Cycling in an Early Earth Analogue: From Ancient Novelty to Modern Commonality

Life emerged and diversified in the absence of molecular oxygen. The prevailing anoxia and unique sulfur chemistry in the Paleo-, Meso-, and Neoarchean and early Proterozoic eras may have supported microbial communities that differ from those currently thriving on the earth's surface. Zodletone spring in southwestern Oklahoma represents a unique habitat where spatial sampling could substitute for geological eras namely, from the anoxic, surficial light-exposed sediments simulating a preoxygenated earth to overlaid water column where air exposure simulates oxygen intrusion during the Neoproterozoic era. We document a remarkably diverse microbial community in the anoxic spring sediments, with 340/516 (65.89%) of genomes recovered in a metagenomic survey belonging to 200 bacterial and archaeal families that were either previously undescribed or that exhibit an extremely rare distribution on the current earth. Such diversity is underpinned by the widespread occurrence of sulfite, thiosulfate, tetrathionate, and sulfur reduction and the paucity of sulfate reduction machineries in these taxa. Hence, these processes greatly expand lineages mediating reductive sulfur-cycling processes in the tree of life. An analysis of the overlaying oxygenated water community demonstrated the development of a significantly less diverse community dominated by well-characterized lineages and a prevalence of oxidative sulfur-cycling processes. Such a transition from ancient novelty to modern commonality underscores the profound impact of the great oxygenation event on the earth's surficial anoxic community. It also suggests that novel and rare lineages encountered in current anaerobic habitats could represent taxa that once thrived in an anoxic earth but have failed to adapt to earth's progressive oxygenation. IMPORTANCE Life on earth evolved in an anoxic setting; however, the identity and fate of microorganisms that thrived in a preoxygenated earth are poorly understood. In Zodletone spring, the prevailing geochemical conditions are remarkably similar to conditions prevailing in surficial earth prior to oxygen buildup in the atmosphere. We identify hundreds of previously unknown microbial lineages in the spring and demonstrate that these lineages possess the metabolic machinery to mediate a wide range of reductive sulfur processes, with the capacity to respire sulfite, thiosulfate, sulfur, and tetrathionate, rather than sulfate, which is a reflection of the differences in sulfur-cycling chemistry in ancient versus modern times. Collectively, such patterns strongly suggest that microbial diversity and sulfur-cycling processes in a preoxygenated earth were drastically different from the currently observed patterns and that the Great Oxygenation Event has precipitated the near extinction of a wide range of oxygen-sensitive lineages and significantly altered the microbial reductive sulfur-cycling community on earth.

An evolutionary perspective on the interplays between hydrogen sulfide and oxygen in cellular functions

The physiological effects of the endogenously generated hydrogen sulfide (H2S) have been extensively studied in recent years. This review summarized the role of H2S in the origin of life and H2S metabolism in organisms from bacteria to vertebrates, examined the relationship between H2S and oxygen from an evolutionary perspective and emphasized the oxygen-dependent manner of H2S signaling in various physiological and pathological processes. H2S and oxygen are inextricably linked in various cellular functions. H2S is involved in aerobic respiration and stimulates oxidative phosphorylation and ATP production within the cell. Besides, H2S has protective effects on ischemia and reperfusion injury in several organs by acting as an oxygen sensor. Also, emerging evidence suggests the role of H2S is in an oxygen-dependent manner. All these findings indicate the subtle relationship between H2S and oxygen and further explain why H2S, a toxic molecule thriving in an anoxia environment several billion years ago, still affects homeostasis today despite the very low content in the body.

Anoxygenic photosynthesis linked to Neoarchean iron formations in Carajás (Brazil)

Microbial activity is often invoked as a direct or indirect contributor to the precipitation of ancient chemical sedimentary rocks such as Precambrian iron formations (IFs). Determining a specific metabolic pathway from the geological record remains a challenge, however, due to a lack of constraints on the initial conditions and microbially induced redox reactions involved in the formation of iron oxides. Thus, there is ongoing debate concerning the role of photoferrotrophy, that is the process by which inorganic carbon is fixed into organic matter using light as an energy source and Fe(II) as an electron donor, in the deposition of IFs. Here, we examine ~2.74-Ga-old Neoarchean IFs and associated carbonates from the Carajás Mineral Province, Brazil, to reconstruct redox conditions and to infer the oxidizing mechanism that allowed one of the world's largest iron deposits to form. The absence of cerium (Ce) anomalies reveals that conditions were pervasively anoxic during IF deposition, while unprecedented europium (Eu) anomalies imply that Fe was supplied by intense hydrothermal activity. A positive and homogeneous Fe isotopic signal in space and time in these IFs indicates a low degree of partial oxidation of Fe(II), which, combined with the presence of ¹³ C-depleted organic matter, points to a photoautotrophic metabolic driver. Collectively, our results argue in favor of reducing conditions during IF deposition and suggest anoxygenic photosynthesis as the most plausible mechanism responsible for Fe oxidation in the Carajás Basin.

Reductive dissolution of pyrite by methanogenic archaea

The formation and fate of pyrite (FeS₂) modulates global iron, sulfur, carbon, and oxygen biogeochemical cycles and has done so since early in Earth’s geological history. A longstanding paradigm is that FeS₂ is stable at low temperature and is unavailable to microorganisms in the absence of oxygen and oxidative weathering. Here, we show that methanogens can catalyze the reductive dissolution of FeS₂ at low temperature (≤38 °C) and utilize dissolution products to meet cellular iron and sulfur demands associated with the biosynthesis of simple and complex co-factors. Direct access to FeS₂ is required to catalyze its reduction and/or to assimilate iron monosulfide that likely forms through coupled reductive dissolution and precipitation, consistent with close associations observed between cells and FeS₂. These findings demonstrate that FeS₂ is bioavailable to anaerobic methanogens and can be mobilized in low temperature anoxic environments. Given that methanogens evolved at least 3.46 Gya, these data indicate that the microbial contribution to the iron and sulfur cycles in ancient and contemporary anoxic environments may be more complex and robust than previously recognized, with impacts on the sources and sinks of iron and sulfur and other bio-essential and thiophilic elements such as nickel and cobalt.

Genomic characterization of three novel Desulfobacterota classes expand the metabolic and phylogenetic diversity of the phylum

We report on the genomic characterization of three novel classes in the phylum Desulfobacterota. One class (proposed name Candidatus 'Anaeroferrophillalia') was characterized by heterotrophic growth capacity, either fermentatively or utilizing polysulfide, tetrathionate or thiosulfate as electron acceptors. In the absence of organic carbon sources, autotrophic growth via the Wood-Ljungdahl (WL) pathway and using hydrogen or Fe(II) as an electron donor is also inferred for members of the 'Anaeroferrophillalia'. The second class (proposed name Candidatus 'Anaeropigmentia') was characterized by its capacity for growth at low oxygen concentration, and the capacity to synthesize the methyl/alkyl carrier CoM, an ability that is prevalent in the archaeal but rare in the bacterial domain. Pigmentation is inferred from the capacity for carotenoid (lycopene) production. The third class (proposed name Candidatus 'Zymogenia') was characterized by fermentative heterotrophic growth capacity, broad substrate range and the adaptation of some of its members to hypersaline habitats. Analysis of the distribution pattern of all three classes showed their occurrence as rare community members in multiple habitats, with preferences for anaerobic terrestrial, freshwater and marine environments over oxygenated (e.g. pelagic ocean and agricultural land) settings. Special preference for some members of the class Candidatus 'Zymogenia' for hypersaline environments such as hypersaline microbial mats and lagoons was observed.

Prebiotic Reaction Networks in Water

A prevailing strategy in origins of life studies is to explore how chemistry constrained by hypothetical prebiotic conditions could have led to molecules and system level processes proposed to be important for life's beginnings. This strategy has yielded model prebiotic reaction networks that elucidate pathways by which relevant compounds can be generated, in some cases, autocatalytically. These prebiotic reaction networks provide a rich platform for further understanding and development of emergent "life-like" behaviours. In this review, recent advances in experimental and analytical procedures associated with classical prebiotic reaction networks, like formose and Miller-Urey, as well as more recent ones are highlighted. Instead of polymeric networks, i.e., those based on nucleic acids or peptides, the focus is on small molecules. The future of prebiotic chemistry lies in better understanding the genuine complexity that can result from reaction networks and the construction of a centralised database of reactions useful for predicting potential network evolution is emphasised.

Temperature limits to deep subseafloor life in the Nankai Trough subduction zone

Microorganisms in marine subsurface sediments substantially contribute to global biomass. Sediments warmer than 40°C account for roughly half the marine sediment volume, but the processes mediated by microbial populations in these hard-to-access environments are poorly understood. We investigated microbial life in up to 1.2-kilometer-deep and up to 120°C hot sediments in the Nankai Trough subduction zone. Above 45°C, concentrations of vegetative cells drop two orders of magnitude and endospores become more than 6000 times more abundant than vegetative cells. Methane is biologically produced and oxidized until sediments reach 80° to 85°C. In 100° to 120°C sediments, isotopic evidence and increased cell concentrations demonstrate the activity of acetate-degrading hyperthermophiles. Above 45°C, populated zones alternate with zones up to 192 meters thick where microbes were undetectable.

In situ S-isotope compositions of sulfate and sulfide from the 3.2 Ga Moodies Group, South Africa: A record of oxidative sulfur cycling

Sulfate minerals are rare in the Archean rock record and largely restricted to the occurrence of barite (BaSO₄ ). The origin of this barite remains controversially debated. The mass-independent fractionation of sulfur isotopes in these and other Archean sedimentary rocks suggests that photolysis of volcanic aerosols in an oxygen-poor atmosphere played an important role in their formation. Here, we report on the multiple sulfur isotopic composition of sedimentary anhydrite in the ca. 3.22 Ga Moodies Group of the Barberton Greenstone Belt, southern Africa. Anhydrite occurs, together with barite and pyrite, in regionally traceable beds that formed in fluvial settings. Variable abundances of barite versus anhydrite reflect changes in sulfate enrichment by evaporitic concentration across orders of magnitude in an arid, nearshore terrestrial environment, periodically replenished by influxes of seawater. The multiple S-isotope compositions of anhydrite and pyrite are consistent with microbial sulfate reduction. S-isotope signatures in barite suggest an additional oxidative sulfate source probably derived from continental weathering of sulfide possibly enhanced by microbial sulfur oxidation. Although depositional environments of Moodies sulfate minerals differ strongly from marine barite deposits, their sulfur isotopic composition is similar and most likely reflects a primary isotopic signature. The data indicate that a constant input of small portions of oxidized sulfur from the continents into the ocean may have contributed to the observed long-term increase in Δ³³ S_sulfate values through the Paleoarchean.

Adenosine-5'-Phosphosulfate- and Sulfite Reductases Activities of Sulfate-Reducing Bacteria from Various Environments

A comparative study of the kinetic characteristics (specific activity, initial and maximum rate, and affinity for substrates) of key enzymes of assimilatory sulfate reduction (APS reductase and dissimilatory sulfite reductase) in cell-free extracts of sulphate-reducing bacteria (SRB) from various biotopes was performed. The material for the study represented different strains of SRB from various ecotopes. Microbiological (isolation and cultivation), biochemical (free cell extract preparation) and chemical (enzyme activity determination) methods served in defining kinetic characteristics of SRB enzymes. The determined affinity data for substrates (i.e., sulfite) were 10 times higher for SRB strains isolated from environmental (soil) ecotopes than for strains from the human intestine. The maximum rate of APS reductase reached 0.282-0.862 µmol/min×mg-1 of protein that is only 10 to 28% higher than similar initial values. The maximum rate of sulfite reductase for corrosive relevant collection strains and SRB strains isolated from heating systems were increased by 3 to 10 times. A completely different picture was found for the intestinal SRB Vmax in the strains Desulfovibrio piger Vib-7 (0.67 µmol/min × mg-1 protein) and Desulfomicrobium orale Rod-9 (0.45 µmol/min × mg-1 protein). The determinant in the cluster distribution of SRB strains is the activity of the terminal enzyme of dissimilatory sulfate reduction-sulfite reductase, but not APS reductase. The data obtained from the activity of sulfate reduction enzymes indicated the adaptive plasticity of SRB strains that is manifested in the change in enzymatic activity.

Mantle data imply a decline of oxidizable volcanic gases could have triggered the Great Oxidation

Aerobic lifeforms, including humans, thrive because of abundant atmospheric O₂, but for much of Earth history O₂ levels were low. Even after evidence for oxygenic photosynthesis appeared, the atmosphere remained anoxic for hundreds of millions of years until the ~2.4 Ga Great Oxidation Event. The delay of atmospheric oxygenation and its timing remain poorly understood. Two recent studies reveal that the mantle gradually oxidized from the Archean onwards, leading to speculation that such oxidation enabled atmospheric oxygenation. But whether this mechanism works has not been quantitatively examined. Here, we show that these data imply that reducing Archean volcanic gases could have prevented atmospheric O₂ from accumulating until ~2.5 Ga with ≥95% probability. For two decades, mantle oxidation has been dismissed as a key driver of the evolution of O₂ and aerobic life. Our findings warrant a reconsideration for Earth and Earth-like exoplanets.

The early Earth’s atmosphere had very low oxygen levels for hundreds of millions of years, until the 2.4 Ga Great Oxidation Event, which remains poorly understood. Here, the authors show that reducing Archean volcanic gases could have prevented atmospheric O₂ from accumulating, and therefore mantle oxidation was likely very important in setting the evolution of O₂ and aerobic life.

Rapid pyritization in the presence of a sulfur/sulfate-reducing bacterial consortium

Sedimentary pyrite (FeS₂) is commonly thought to be a product of microbial sulfate reduction and hence may preserve biosignatures. However, proof that microorganisms are involved in pyrite formation is still lacking as only metastable iron sulfides are usually obtained in laboratory cultures. Here we show the rapid formation of large pyrite spherules through the sulfidation of Fe(III)-phosphate (FP) in the presence of a consortium of sulfur- and sulfate-reducing bacteria (SRB), Desulfovibrio and Sulfurospirillum, enriched from ferruginous and phosphate-rich Lake Pavin water. In biomineralization experiments inoculated with this consortium, pyrite formation occurred within only 3 weeks, likely enhanced by the local enrichment of polysulfides around SRB cells. During this same time frame, abiotic reaction of FP with sulfide led to the formation of vivianite (Fe₃(PO₄)₂·8H₂O) and mackinawite (FeS) only. Our results suggest that rates of pyritization vs. vivianite formation are regulated by SRB activity at the cellular scale, which enhances phosphate release into the aqueous phase by increased efficiency of iron sulfide precipitation, and thus that these microorganisms strongly influence biological productivity and Fe, S and P cycles in the environment.

Phylogenomic analysis of novel Diaforarchaea is consistent with sulfite but not sulfate reduction in volcanic environments on early Earth

The origin(s) of dissimilatory sulfate and/or (bi)sulfite reducing organisms (SRO) remains enigmatic despite their importance in global carbon and sulfur cycling since at least 3.4 Ga. Here, we describe novel, deep-branching archaeal SRO populations distantly related to other Diaforarchaea from two moderately acidic thermal springs. Dissimilatory (bi)sulfite reductase homologs, DsrABC, encoded in metagenome assembled genomes (MAGs) from spring sediments comprise one of the earliest evolving Dsr lineages. DsrA homologs were expressed in situ under moderately acidic conditions. MAGs lacked genes encoding proteins that activate sulfate prior to (bi)sulfite reduction. This is consistent with sulfide production in enrichment cultures provided sulfite but not sulfate. We suggest input of volcanic sulfur dioxide to anoxic spring-water yields (bi)sulfite and moderately acidic conditions that favor its stability and bioavailability. The presence of similar volcanic springs at the time SRO are thought to have originated (>3.4 Ga) may have supplied (bi)sulfite that supported ancestral SRO. These observations coincide with the lack of inferred SO42- reduction capacity in nearly all organisms with early-branching DsrAB and which are near universally found in hydrothermal environments.

The effect of temperature on sulfur and oxygen isotope fractionation by sulfate reducing bacteria (Desulfococcus multivorans)

Temperature influences microbiological growth and catabolic rates. Between 15 and 35 °C the growth rate and cell specific sulfate reduction rate of the sulfate reducing bacterium Desulfococcus multivorans increased with temperature. Sulfur isotope fractionation during sulfate reduction decreased with increasing temperature from 27.2 ‰ at 15 °C to 18.8 ‰ at 35 °C which is consistent with a decreasing reversibility of the metabolic pathway as the catabolic rate increases. Oxygen isotope fractionation, in contrast, decreased between 15 and 25 °C and then increased again between 25 and 35 °C, suggesting increasing reversibility in the first steps of the sulfate reducing pathway at higher temperatures. This points to a decoupling in the reversibility of sulfate reduction between the steps from the uptake of sulfate into the cell to the formation of sulfite, relative to the whole pathway from sulfate to sulfide. This observation is consistent with observations of increasing sulfur isotope fractionation when sulfate reducing bacteria are living near their upper temperature limit. The oxygen isotope decoupling may be a first signal of changing physiology as the bacteria cope with higher temperatures.

Global atmospheric oxygen variations recorded by Th/U systematics of igneous rocks

Scientists have been working on the dating of atmospheric oxygenation in Earth’s history for decades. However, most previous studies relied on evidence from sedimentary rocks. Here, we show that igneous rocks can also be linked with surface oxidation by a key geological process: plate subduction. We here make an attempt to apply the Th/U of worldwide arc igneous rocks as an indicator for the timing of atmospheric oxygenation over the Earth’s history. The results are coincident with the previously defined Great Oxidation Event and Neoproterozoic Oxygenation Event.

Atmospheric oxygen has evolved from negligible levels in the Archean to the current level of about 21% through 2 major step rises: The Great Oxidation Event (GOE) in the early Proterozoic and the Neoproterozoic Oxygenation Event (NOE) during the late Proterozoic. However, most previous methods for constraining the time of atmospheric oxygenation have relied on evidence from sedimentary rocks. Here, we investigate the temporal variations of the Th/U of arc igneous rocks since 3.0 billion y ago (Ga) and show that 2 major Th/U decreases are recorded at ca. 2.35 Ga and ca. 0.75 Ga, coincident with the beginning of the GOE and NOE. The decoupling of U from Th is predominantly caused by the significant rise of atmospheric oxygen. Under an increasingly oxidized atmosphere condition, more uranium in the surface environment became oxidized from the water-insoluble U⁴⁺ to the water-soluble U⁶⁺ valance and incorporated in the sea water and altered oceanic crust. Eventually, the subduction of this altered oceanic crust produced the low-Th/U signature of arc igneous rocks. Therefore, the sharp decrease of Th/U in global arc igneous rocks may provide strong evidence for the rise of atmospheric oxygen. We suggest that the secular Th/U evolution of arc igneous rocks could be an effective geochemical indicator recording the global-scale atmospheric oxygen variation.

Hydrogen sulfide, reactive sulfur species and coping with reactive oxygen species

Life began in a ferruginous (anoxic and Fe²⁺ dominated) world around 3.8 billion years ago (bya). Hydrogen sulfide (H₂S) and other sulfur molecules from hydrothermal vents and other fissures provided many key necessities for life's origin including catalytic platforms (primordial enzymes) that also served as primitive boundaries (cell walls), substrates for organic synthesis and a continuous source of energy in the form of reducing equivalents. Anoxigenic photosynthesis oxidizing H₂S followed within a few hundred million years and laid the metabolic groundwork for oxidative photosynthesis some half-billion years later that slightly and episodically increased atmospheric oxygen around 2.3 bya. This oxidized terrestrial sulfur to sulfate which was washed to the sea where it was reduced creating vast euxinic (anoxic and sulfidic) areas. It was in this environment that eukaryotic cells appeared around 1.5 bya and where they evolved for nearly 1 billion additional years. Oxidative photosynthesis finally oxidized the oceans and around 0.6 bya oxygen levels in the atmosphere and oceans began to rise toward present day levels. This is purported to have been a life-threatening event due to the prevalence of reactive oxygen species (ROS) and thus necessitated the elaboration of chemical and enzymatic antioxidant mechanisms. However, these antioxidants initially appeared around the time of anoxigenic photosynthesis suggesting a commitment to metabolism of reactive sulfur species (RSS). This review examines these events and suggests that many of the biological attributes assigned to ROS may, in fact, be due to RSS. This is underscored by observations that ROS and RSS are chemically similar, often indistinguishable by analytical methods and the fact that the bulk of biochemical and physiological experiments are performed in unphysiologically oxic environments where ROS are artifactually favored over RSS.

Hypoxia Rescues Frataxin Loss by Restoring Iron Sulfur Cluster Biogenesis

Friedreich's ataxia (FRDA) is a devastating, multisystemic disorder caused by recessive mutations in the mitochondrial protein frataxin (FXN). FXN participates in the biosynthesis of Fe-S clusters and is considered to be essential for viability. Here we report that when grown in 1% ambient O2, FXN null yeast, human cells, and nematodes are fully viable. In human cells, hypoxia restores steady-state levels of Fe-S clusters and normalizes ATF4, NRF2, and IRP2 signaling events associated with FRDA. Cellular studies and in vitro reconstitution indicate that hypoxia acts through HIF-independent mechanisms that increase bioavailable iron as well as directly activate Fe-S synthesis. In a mouse model of FRDA, breathing 11% O2 attenuates the progression of ataxia, whereas breathing 55% O2 hastens it. Our work identifies oxygen as a key environmental variable in the pathogenesis associated with FXN depletion, with important mechanistic and therapeutic implications.

Effects of inhibiting antioxidant pathways on cellular hydrogen sulfide and polysulfide metabolism

Elaborate antioxidant pathways have evolved to minimize the threat of excessive reactive oxygen species (ROS) and to regulate ROS as signaling entities. ROS are chemically and functionally similar to reactive sulfur species (RSS) and both ROS and RSS have been shown to be metabolized by the antioxidant enzymes, superoxide dismutase and catalase. Here we use fluorophores to examine the effects of a variety of inhibitors of antioxidant pathways on metabolism of two important RSS, hydrogen sulfide (H₂S with AzMC) and polysulfides (H₂S_n, where n = 2-7, with SSP4) in HEK293 cells. Cells were exposed to inhibitors for up to 5 days in normoxia (21% O₂) and hypoxia (5% O₂), conditions also known to affect ROS production. Decreasing intracellular glutathione (GSH) with l-buthionine-sulfoximine (BSO) or diethyl maleate (DEM) decreased H₂S production for 5 days but did not affect H₂S_n. The glutathione reductase inhibitor, auranofin, initially decreased H₂S and H₂S_n but after two days H₂S_n increased over controls. Inhibition of peroxiredoxins with conoidin A decreased H₂S and increased H₂S_n, whereas the glutathione peroxidase inhibitor, tiopronin, increased H₂S. Aminoadipic acid, an inhibitor of cystine uptake did not affect either H₂S or H₂S_n. In buffer, the glutathione reductase and thioredoxin reductase inhibitor, 2-AAPA, the glutathione peroxidase mimetic, ebselen, and tiopronin variously reacted directly with AzMC and SSP4, reacted with H₂S and H₂S₂, or optically interfered with AzMC or SSP4 fluorescence. Collectively these results show that antioxidant inhibitors, generally known for their ability to increase cellular ROS, have various effects on cellular RSS. These findings suggest that the inhibitors may affect cellular sulfur metabolism pathways that are not related to ROS production and in some instances they may directly affect RSS or the methods used to measure them. They also illustrate the importance of carefully evaluating RSS metabolism when biologically or pharmacologically attempting to manipulate ROS.

O2 affects mitochondrial functionality ex vivo

Mitochondria have originated in eukaryotic cells by endosymbiosis of a specialized prokaryote approximately 2 billion years ago. They are essential for normal cell function by providing energy through their role in oxidizing carbon substrates. Glutathione (GSH) is a major thiol-disulfide redox buffer of the cell including the mitochondrial matrix and intermembrane space. We have generated cardiomyocyte-specific Grx1-roGFP2 GSH redox potential (E_GSH) biosensor mice in the past, in which the sensor is targeted to the mitochondrial matrix. Using this mouse model a distinct E_GSH of the mitochondrial matrix (−278.9 ± 0.4 mV) in isolated cardiomyocytes is observed. When analyzing the E_GSH in isolated mitochondria from the transgenic hearts, however, the E_GSH in the mitochondrial matrix is significantly oxidized (−247.7 ± 8.7 mV). This is prevented by adding N-Ethylmaleimide during the mitochondria isolation procedure, which precludes disulfide bond formation. A similar reducing effect is observed by isolating mitochondria in hypoxic (0.1–3% O₂) conditions that mimics mitochondrial pO₂ levels in cellulo. The reduced E_GSH is accompanied by lower ROS production, reduced complex III activity but increased ATP levels produced at baseline and after stimulation with succinate/ADP. Altogether, we demonstrate that oxygenation is an essential factor that needs to be considered when analyzing mitochondrial function ex vivo.

•

We identified that mitochondria isolated in room air at 20.9% O₂ exhibit a strong oxidation of the E_GSH in the matrix.

•

Isolation of mitochondria in hypoxic conditions mimicking their in cellulo conditions prevents oxidation of the E_GSH.

•

Normoxic and hypoxic isolated mitochondria differ in ROS production, complex III activity and ATP levels.

•

Oxygenation needs to be considered when analyzing mitochondrial function ex vivo.

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate/sulfite reduction in the genomes of organisms from 13 bacterial and archaeal phyla, thereby more than doubling the number of microbial phyla associated with this process. Eight of the 13 newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Organisms from Verrucomicrobia and two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota, contain some of the earliest evolved dsrAB genes. The capacity for sulfite reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of modulating sulfur metabolism in associated cells has been acquired by putatively symbiotic bacteria. We conclude that current functional predictions based on phylogeny significantly underestimate the extent of sulfate/sulfite reduction across Earth's ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.

1H-NMR as implemented in several origin of life studies artificially implies the absence of metabolism-like non-enzymatic reactions by being signal-suppressed

Background. Life depends on small subsets of chemically possible reactions. A chemical process can hence be prebiotically plausible, yet be unrelated to the origins of life. An example is the synthesis of nucleotides from hydrogen cyanide, considered prebiotically plausible, but incompatible with metabolic evolution. In contrast, only few metabolism-compatible prebiotic reactions were known until recently. Here, we question whether technical limitations may have contributed to the situation. Methods: Enzymes evolved to accelerate and control biochemical reactions. This situation dictates that compared to modern metabolic pathways, precursors to enzymatic reactions have been slower and less efficient, yielding lower metabolite quantities. This situation demands for the application of highly sensitive analytical techniques for studying ‘proto-metabolism’. We noticed that a set of proto-metabolism studies derive conclusions from the absence of metabolism-like signals, yet do not report detection limits. We here benchmark the respective 1H-NMR implementation for the ability to detect Krebs cycle intermediates, considered examples of plausible metabolic precursors. Results: Compared to metabolomics ‘gold-standard’ methods, 1H-NMR as implemented is i) at least one hundred- to thousand-fold less sensitive, ii) prone to selective metabolite loss, and iii) subject to signal suppression by Fe(II) concentrations as extrapolated from Archean sediment. In sum these restrictions mount to huge sensitivity deficits, so that even highly concentrated Krebs cycle intermediates are rendered undetectable unless the method is altered to boost sensitivity. Conclusions 1H-NMR as implemented in several origin of life studies does not achieve the sensitivity to detect cellular metabolite concentrations, let alone evolutionary precursors at even lower concentration. These studies can hence not serve as proof-of-absence for metabolism-like reactions. Origin of life theories that essentially depend on this assumption, i.e. those that consider proto-metabolism to consist of non-metabolism-like reactions derived from non-metabolic precursors like hydrogen cyanide, may have been derived from a misinterpretation of negative analytical results.

Oxidative alteration of ferrous smectites and implications for the redox evolution of early Mars

Surface conditions on early Mars were likely anoxic, similar to early Earth, but the timing of the evolution to oxic conditions characteristic of contemporary Mars is unresolved. Ferrous trioctahedral smectites are the thermodynamically predicted products of anoxic basalt weathering, but orbital analyses of Noachian-aged terrains find primarily Fe3+-bearing clay minerals. Rover-based detection of Fe2+-bearing trioctahedral smectites at Gale Crater suggest that ferrous smectites are the unoxidized progenitors of orbitally-detected ferric smectites. To assess this pathway, we conducted ambient-temperature oxidative alteration experiments on four synthetic ferrous smectites having molar Fe/(Mg+Fe) from 1.00 to 0.33. Smectite suspension in air-saturated solutions produced incomplete oxidation (24-38% Fe3+/ΣFe). Additional smectite oxidation occurred upon re-exposure to air-saturated solutions after anoxic hydrothermal recrystallization, which accelerated cation and charge redistribution in the octahedral sheet. Oxidation was accompanied by contraction of the octahedral sheet (d(060) decreased from 1.53-1.56 Å to 1.52 Å), consistent with a shift towards dioctahedral structure. Ferrous smectite oxidation by aqueous hydrogen peroxide solutions resulted in nearly complete Fe2+ oxidation but also led to partial Fe3+ ejection from the structure, producing nanoparticulate hematite. Reflectance spectra of oxidized smectites were characterized by (Fe3+,Mg)2-OH bands at 2.28-2.30 μm, consistent with oxidative formation of dioctahedral nontronite. Accordingly, ferrous smectites are plausible precursors to observed ferric smectites on Mars, and their presence in late-Noachian sedimentary units suggests that anoxic conditions may have persisted on Mars beyond the Noachian.

Microbial acceleration of aerobic pyrite oxidation at circumneutral pH

Pyrite (FeS₂ ) is the most abundant sulfide mineral on Earth and represents a significant reservoir of reduced iron and sulfur both today and in the geologic past. In modern environments, oxidative transformations of pyrite and other metal sulfides play a key role in terrestrial element partitioning with broad impacts to contaminant mobility and the formation of acid mine drainage systems. Although the role of aerobic micro-organisms in pyrite oxidation under acidic-pH conditions is well known, to date there is very little known about the capacity for aerobic micro-organisms to oxidize pyrite at circumneutral pH. Here, we describe two enrichment cultures, obtained from pyrite-bearing subsurface sediments, that were capable of sustained cell growth linked to pyrite oxidation and sulfate generation at neutral pH. The cultures were dominated by two Rhizobiales species (Bradyrhizobium sp. and Mesorhizobium sp.) and a Ralstonia species. Shotgun metagenomic sequencing and genome reconstruction indicated the presence of Fe and S oxidation pathways in these organisms, and the presence of a complete Calvin-Benson-Bassham CO₂ fixation system in the Bradyrhizobium sp. Oxidation of pyrite resulted in thin (30-50 nm) coatings of amorphous Fe(III) oxide on the pyrite surface, with no other secondary Fe or S phases detected by electron microscopy or X-ray absorption spectroscopy. Rates of microbial pyrite oxidation were approximately one order of magnitude higher than abiotic rates. These results demonstrate the ability of aerobic microbial activity to accelerate pyrite oxidation and expand the potential contribution of micro-organisms to continental sulfide mineral weathering around the time of the Great Oxidation Event to include neutral-pH environments. In addition, our findings have direct implications for the geochemistry of modern sedimentary environments, including stimulation of the early stages of acid mine drainage formation and mobilization of pyrite-associated metals.

Primordial Krebs-cycle-like non-enzymatic reactions detected by mass spectrometry and nuclear magnetic resonance

Background: Metabolism is the process of nutrient uptake and conversion, and executed by the metabolic network. Its evolutionary precursors most likely originated in non-enzymatic chemistry. To be exploitable in a Darwinian process that forms a metabolic pathway, non-enzymatic reactions need to form a chemical network that produces advantage-providing metabolites in a single, life compatible condition. In a hypothesis-generating, large-scale experiment, we recently screened iron and sulfur-rich solutions, and report that upon the formation of sulfate radicals, Krebs cycle intermediates establish metabolism-like non-enzymatic reactivity. A challenge to our results claims that the results obtained by liquid chromatography-selective reaction monitoring (LC-SRM) would not be reproducible by nuclear magnetic resonance spectroscopy (1H-NMR). Methods: This study compared the application of the two techniques to the relevant samples. Results: We detect hundred- to thousand-fold differences in the specific limits of detection between LC-SRM and 1H-NMR to detect Krebs cycle intermediates. Further, the use of 1H-NMR was found generally problematic to characterize early metabolic reactions, as Archean-sediment typical iron concentrations cause paramagnetic signal suppression. Consequently, we selected non-enzymatic Krebs cycle reactions that fall within the determined technical limits. We confirm that these proceed unequivocally as evidenced by both LC-SRM and 1H-NMR. Conclusions: These results strengthen our previous conclusions about the existence of unifying reaction conditions that enables a series of co-occurring metabolism-like non-enzymatic Krebs cycle reactions. We further discuss why constraints applying to metabolism disentangle concentration from importance of any reaction intermediates, and why evolutionary precursors to metabolic pathways must have had much lower metabolite concentrations compared to modern metabolic networks. Research into the chemical origins of life will hence miss out on the chemistry relevant for metabolism if its focus is restricted solely to highly abundant and unreactive metabolites, including when it ignores life-compatibility of the reaction conditions as an essential constraint in enzyme evolution.

Influence of Phosphorus and Cell Geometry on the Fractionation of Sulfur Isotopes by Several Species of Desulfovibrio during Microbial Sulfate Reduction

We investigated the influence of organic substrates and phosphate concentration on the rates of dissimilatory microbial sulfate reduction and the ³⁴S/³²S isotopic fractionation produced by several Desulfovibrio species. Our experiments corroborate the previously reported species-specific correlation between sulfur isotope fractionation and cell-specific sulfate reduction rates. We also identify cell size as a key factor that contributes to the species-effect of this correlation. Phosphate limitation results in larger cells and contributes to a small decrease in sulfur isotope fractionation concomitant with an apparent increase in cell-specific sulfate reduction rates. Sulfur isotope fractionation in phosphate-limited cultures asymptotically approaches a lower limit of approximately 5‰ as cell-specific sulfate reduction rates increase to >100 fmol cell⁻¹ day⁻¹. These experimental results test models that link the reversibilities of enzymatic steps in dissimilatory sulfate reduction to sulfur isotope fractionation and show that these models can provide consistent predictions across large variations in physiological states experienced by sulfate reducing bacteria.

The Neoarchaean surficial sulphur cycle: An alternative hypothesis based on analogies with 20th-century atmospheric lead

We revisit the S-isotope systematics of sedimentary pyrite in a shaly limestone from the ca. 2.52 Ga Gamohaan Formation, Upper Campbellrand Subgroup, Transvaal, South Africa. The analysed rock is interpreted to have been deposited in a water depth of ca. 50-100 m, in a restricted sub-basin on a drowning platform. A previous study discovered that the pyrites define a nonzero intercept δ³⁴ S_V-CDT -Δ³³ S data array. The present study carried out further quadruple S-isotope analyses of pyrite, confirming and expanding the linear δ³⁴ S_V-CDT -Δ³³ S array with an δ³⁴ S zero intercept at ∆³³ S ca. +5. This was previously interpreted to indicate mixing of unrelated S-sources in the sediment environment, involving a combination of recycled sulphur from sulphides that had originally formed by sulphate-reducing bacteria, along with elemental sulphur. Here, we advance an alternative explanation based on the recognition that the Archaean seawater sulphate concentration was likely very low, implying that the Archaean ocean could have been poorly mixed with respect to sulphur. Thus, modern oceanic sulphur systematics provide limited insight into the Archaean sulphur cycle. Instead, we propose that the 20th-century atmospheric lead event may be a useful analogue. Similar to industrial lead, the main oceanic input of Archaean sulphur was through atmospheric raindown, with individual giant point sources capable of temporally dominating atmospheric input. Local atmospheric S-isotope signals, of no global significance, could thus have been transmitted into the localised sediment record. Thus, the nonzero intercept δ³⁴ S_V-CDT -Δ³³ S data array may alternatively represent a very localised S-isotope signature in the Neoarchaean surface environment. Fallout from local volcanic eruptions could imprint recycled MIF-S signals into pyrite of restricted depositional environments, thereby avoiding attenuation of the signal in the subdued, averaged global open ocean sulphur pool. Thus, the superposition of extreme local S-isotope signals offers an alternative explanation for the large Neoarchaean MIF-S excursions and asymmetry of the Δ³³ S rock record.

Sulfate radicals enable a non-enzymatic Krebs cycle precursor

The evolutionary origins of the tricarboxylic acid cycle (TCA), or Krebs cycle, are so far unclear. Despite a few years ago, the existence of a simple non-enzymatic Krebs-cycle catalyst has been dismissed 'as an appeal to magic', citrate and other intermediates have meanwhile been discovered on a carbonaceous meteorite and do interconvert non-enzymatically. To identify the non-enzymatic Krebs cycle catalyst, we used combinatorial, quantitative high-throughput metabolomics to systematically screen iron and sulfate reaction milieus that orient on Archean sediment constituents. TCA cycle intermediates are found stable in water and in the presence of most iron and sulfate species, including simple iron-sulfate minerals. However, we report that TCA intermediates undergo 24 interconversion reactions in the presence of sulfate radicals that form from peroxydisulfate. The non-enzymatic reactions critically cover a topology as present in the Krebs cycle, the glyoxylate shunt and the succinic semialdehyde pathways. Assembled in a chemical network, the reactions achieve more than ninety percent carbon recovery. Our results show that a non-enzymatic precursor for the Krebs cycle is biologically sensible, efficient, and forms spontaneously in the presence of sulfate radicals.

Conditional iron and pH-dependent activity of a non-enzymatic glycolysis and pentose phosphate pathway

Little is known about the evolutionary origins of metabolism. However, key biochemical reactions of glycolysis and the pentose phosphate pathway (PPP), ancient metabolic pathways central to the metabolic network, have non-enzymatic pendants that occur in a prebiotically plausible reaction milieu reconstituted to contain Archean sediment metal components. These non-enzymatic reactions could have given rise to the origin of glycolysis and the PPP during early evolution. Using nuclear magnetic resonance spectroscopy and high-content metabolomics that allowed us to measure several thousand reaction mixtures, we experimentally address the chemical logic of a metabolism-like network constituted from these non-enzymatic reactions. Fe(II), the dominant transition metal component of Archean oceanic sediments, has binding affinity toward metabolic sugar phosphates and drives metabolism-like reactivity acting as both catalyst and cosubstrate. Iron and pH dependencies determine a metabolism-like network topology and comediate reaction rates over several orders of magnitude so that the network adopts conditional activity. Alkaline pH triggered the activity of the non-enzymatic PPP pendant, whereas gentle acidic or neutral conditions favored non-enzymatic glycolytic reactions. Fe(II)-sensitive glycolytic and PPP-like reactions thus form a chemical network mimicking structural features of extant carbon metabolism, including topology, pH dependency, and conditional reactivity. Chemical networks that obtain structure and catalysis on the basis of transition metals found in Archean sediments are hence plausible direct precursors of cellular metabolic networks.

Evolutionary History of the Photolyase/Cryptochrome Superfamily in Eukaryotes

BACKGROUND

Photolyases and cryptochromes are evolutionarily related flavoproteins, which however perform distinct physiological functions. Photolyases (PHR) are evolutionarily ancient enzymes. They are activated by light and repair DNA damage caused by UV radiation. Although cryptochromes share structural similarity with DNA photolyases, they lack DNA repair activity. Cryptochrome (CRY) is one of the key elements of the circadian system in animals. In plants, CRY acts as a blue light receptor to entrain circadian rhythms, and mediates a variety of light responses, such as the regulation of flowering and seedling growth.

RESULTS

We performed a comprehensive evolutionary analysis of the CRY/PHR superfamily. The superfamily consists of 7 major subfamilies: CPD class I and CPD class II photolyases, (6-4) photolyases, CRY-DASH, plant PHR2, plant CRY and animal CRY. Although the whole superfamily evolved primarily under strong purifying selection (average ω = 0.0168), some subfamilies did experience strong episodic positive selection during their evolution. Photolyases were lost in higher animals that suggests natural selection apparently became weaker in the late stage of evolutionary history. The evolutionary time estimates suggested that plant and animal CRYs evolved in the Neoproterozoic Era (~1000-541 Mya), which might be a result of adaptation to the major climate and global light regime changes occurred in that period of the Earth's geological history.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.

The RNA world and the origin of metabolic enzymes

An RNA world has been placed centre stage for explaining the origin of life. Indeed, RNA is the most plausible molecule able to form both a (self)-replicator and to inherit information, necessities for initiating genetics. However, in parallel with self-replication, the proto-organism had to obtain the ability to catalyse supply of its chemical constituents, including the ribonucleotide metabolites required to replicate RNA. Although the possibility of an RNA-catalysed metabolic network has been considered, it is to be questioned whether RNA molecules, at least on their own, possess the required catalytic capacities. An alternative scenario for the origin of metabolism involves chemical reactions that are based on environmental catalysts. Recently, we described a non-enzymatic glycolysis and pentose phosphate pathway-like reactions catalysed by metal ions [mainly Fe(II)] and phosphate, simple inorganic molecules abundantly found in Archaean sediments. While the RNA world can serve to explain the origin of genetics, the origin of the metabolic network might thus date back to constraints of environmental chemistry. Interestingly, considering a metal-catalysed origin of metabolism gives rise to an attractive hypothesis about how the first enzymes could have formed: simple RNA or (poly)peptide molecules could have bound the metal ions, and thus increased their solubility, concentration and accessibility. In a second step, this would have allowed substrate specificity to evolve.

Sulfur-cycling fossil bacteria from the 1.8-Ga Duck Creek Formation provide promising evidence of evolution's null hypothesis

The recent discovery of a deep-water sulfur-cycling microbial biota in the ∼ 2.3-Ga Western Australian Turee Creek Group opened a new window to life's early history. We now report a second such subseafloor-inhabiting community from the Western Australian ∼ 1.8-Ga Duck Creek Formation. Permineralized in cherts formed during and soon after the 2.4- to 2.2-Ga "Great Oxidation Event," these two biotas may evidence an opportunistic response to the mid-Precambrian increase of environmental oxygen that resulted in increased production of metabolically useable sulfate and nitrate. The marked similarity of microbial morphology, habitat, and organization of these fossil communities to their modern counterparts documents exceptionally slow (hypobradytelic) change that, if paralleled by their molecular biology, would evidence extreme evolutionary stasis.