Biogenic methane, hydrogen escape, and the irreversible oxidation of early Earth

Photosynthesis in the Archean era

The earliest reductant for photosynthesis may have been H2. The carbon isotope composition measured in graphite from the 3.8-Ga Isua Supercrustal Belt in Greenland is attributed to H2-driven photosynthesis, rather than to oxygenic photosynthesis as there would have been no evolutionary pressure for oxygenic photosynthesis in the presence of H2. Anoxygenic photosynthesis may also be responsible for the filamentous mats found in the 3.4-Ga Buck Reef Chert in South Africa. Another early reductant was probably H2S. Eventually the supply of H2 in the atmosphere was likely to have been attenuated by the production of CH4 by methanogens, and the supply of H2S was likely to have been restricted to special environments near volcanos. Evaporites, possible stromatolites, and possible microfossils found in the 3.5-Ga Warrawoona Megasequence in Australia are attributed to sulfur-driven photosynthesis. Proteobacteria and protocyanobacteria are assumed to have evolved to use ferrous iron as reductant sometime around 3.0 Ga or earlier. This type of photosynthesis could have produced banded iron formations similar to those produced by oxygenic photosynthesis. Microfossils, stromatolites, and chemical biomarkers in Australia and South Africa show that cyanobacteria containing chlorophyll a and carrying out oxygenic photosynthesis appeared by 2.8 Ga, but the oxygen level in the atmosphere did not begin to increase until about 2.3 Ga.

The Paleoproterozoic snowball Earth: a climate disaster triggered by the evolution of oxygenic photosynthesis

Although biomarker, trace element, and isotopic evidence have been used to claim that oxygenic photosynthesis evolved by 2.8 giga-annum before present (Ga) and perhaps as early as 3.7 Ga, a skeptical examination raises considerable doubt about the presence of oxygen producers at these times. Geological features suggestive of oxygen, such as red beds, lateritic paleosols, and the return of sedimentary sulfate deposits after a approximately 900-million year hiatus, occur shortly before the approximately 2.3-2.2 Ga Makganyene "snowball Earth" (global glaciation). The massive deposition of Mn, which has a high redox potential, practically requires the presence of environmental oxygen after the snowball. New age constraints from the Transvaal Supergroup of South Africa suggest that all three glaciations in the Huronian Supergroup of Canada predate the Snowball event. A simple cyanobacterial growth model incorporating the range of C, Fe, and P fluxes expected during a partial glaciation in an anoxic world with high-Fe oceans indicates that oxygenic photosynthesis could have destroyed a methane greenhouse and triggered a snowball event on time-scales as short as 1 million years. As the geological evidence requiring oxygen does not appear during the Pongola glaciation at 2.9 Ga or during the Huronian glaciations, we argue that oxygenic cyanobacteria evolved and radiated shortly before the Makganyene snowball.

Why O2 is required by complex life on habitable planets and the concept of planetary "oxygenation time"

Life is constructed from a limited toolkit: the Periodic Table. The reduction of oxygen provides the largest free energy release per electron transfer, except for the reduction of fluorine and chlorine. However, the bonding of O2 ensures that it is sufficiently stable to accumulate in a planetary atmosphere, whereas the more weakly bonded halogen gases are far too reactive ever to achieve significant abundance. Consequently, an atmosphere rich in O2 provides the largest feasible energy source. This universal uniqueness suggests that abundant O2 is necessary for the high-energy demands of complex life anywhere, i.e., for actively mobile organisms of approximately 10(-1)-10(0) m size scale with specialized, differentiated anatomy comparable to advanced metazoans. On Earth, aerobic metabolism provides about an order of magnitude more energy for a given intake of food than anaerobic metabolism. As a result, anaerobes do not grow beyond the complexity of uniseriate filaments of cells because of prohibitively low growth efficiencies in a food chain. The biomass cumulative number density, n, at a particular mass, m, scales as n (> m) proportional to m(-1) for aquatic aerobes, and we show that for anaerobes the predicted scaling is n proportional to m (-1.5), close to a growth-limited threshold. Even with aerobic metabolism, the partial pressure of atmospheric O2 (P(O2)) must exceed approximately 10(3) Pa to allow organisms that rely on O2 diffusion to evolve to a size approximately 10(3) m x P(O2) in the range approximately 10(3)-10(4) Pa is needed to exceed the threshold of approximately 10(2) m size for complex life with circulatory physiology. In terrestrial life, O(2) also facilitates hundreds of metabolic pathways, including those that make specialized structural molecules found only in animals. The time scale to reach P(O(2)) approximately 10(4) Pa, or "oxygenation time," was long on the Earth (approximately 3.9 billion years), within almost a factor of 2 of the Sun's main sequence lifetime. Consequently, we argue that the oxygenation time is likely to be a key rate-limiting step in the evolution of complex life on other habitable planets. The oxygenation time could preclude complex life on Earth-like planets orbiting short-lived stars that end their main sequence lives before planetary oxygenation takes place. Conversely, Earth-like planets orbiting long-lived stars are potentially favorable habitats for complex life.

Evidence from massive siderite beds for a CO2-rich atmosphere before approximately 1.8 billion years ago

It is generally thought that, in order to compensate for lower solar flux and maintain liquid oceans on the early Earth, methane must have been an important greenhouse gas before approximately 2.2 billion years (Gyr) ago. This is based upon a simple thermodynamic calculation that relates the absence of siderite (FeCO3) in some pre-2.2-Gyr palaeosols to atmospheric CO2 concentrations that would have been too low to have provided the necessary greenhouse effect. Using multi-dimensional thermodynamic analyses and geological evidence, we show here that the absence of siderite in palaeosols does not constrain atmospheric CO2 concentrations. Siderite is absent in many palaeosols (both pre- and post-2.2-Gyr in age) because the O2 concentrations and pH conditions in well-aerated soils have favoured the formation of ferric (Fe3+)-rich minerals, such as goethite, rather than siderite. Siderite, however, has formed throughout geological history in subsurface environments, such as euxinic seas, where anaerobic organisms created H2-rich conditions. The abundance of large, massive siderite-rich beds in pre-1.8-Gyr sedimentary sequences and their carbon isotope ratios indicate that the atmospheric CO2 concentration was more than 100 times greater than today, causing the rain and ocean waters to be more acidic than today. We therefore conclude that CO2 alone (without a significant contribution from methane) could have provided the necessary greenhouse effect to maintain liquid oceans on the early Earth.

A lower limit for atmospheric carbon dioxide levels 3.2 billion years ago

The quantification of greenhouse gases present in the Archaean atmosphere is critical for understanding the evolution of atmospheric oxygen, surface temperatures and the conditions for life on early Earth. For instance, it has been argued that small changes in the balance between two potential greenhouse gases, carbon dioxide and methane, may have dictated the feedback cycle involving organic haze production and global cooling. Climate models have focused on carbon dioxide as the greenhouse gas responsible for maintaining above-freezing surface temperatures during a time of low solar luminosity. However, the analysis of 2.75-billion-year (Gyr)-old palaeosols--soil samples preserved in the geologic record--have recently provided an upper constraint on atmospheric carbon dioxide levels well below that required in most climate models to prevent the Earth's surface from freezing. This finding prompted many to look towards methane as an additional greenhouse gas to satisfy climate models. Here we use model equilibrium reactions for weathering rinds on 3.2-Gyr-old river gravels to show that the presence of iron-rich carbonate relative to common clay minerals requires a minimum partial pressure of carbon dioxide several times higher than present-day values. Unless actual carbon dioxide levels were considerably greater than this, climate models predict that additional greenhouse gases would still need to have a role in maintaining above-freezing surface temperatures.

The Natural History of Nitrogen Fixation

In recent years, our understanding of biological nitrogen fixation has been bolstered by a diverse array of scientific techniques. Still, the origin and extant distribution of nitrogen fixation has been perplexing from a phylogenetic perspective, largely because of factors that confound molecular phylogeny such as sequence divergence, paralogy, and horizontal gene transfer. Here, we make use of 110 publicly available complete genome sequences to understand how the core components of nitrogenase, including NifH, NifD, NifK, NifE, and NifN proteins, have evolved. These genes are universal in nitrogen fixing organisms-typically found within highly conserved operons-and, overall, have remarkably congruent phylogenetic histories. Additional clues to the early origins of this system are available from two distinct clades of nitrogenase paralogs: a group composed of genes essential to photosynthetic pigment biosynthesis and a group of uncharacterized genes present in methanogens and in some photosynthetic bacteria. We explore the complex genetic history of the nitrogenase family, which is replete with gene duplication, recruitment, fusion, and horizontal gene transfer and discuss these events in light of the hypothesized presence of nitrogenase in the last common ancestor of modern organisms, as well as the additional possibility that nitrogen fixation might have evolved later, perhaps in methanogenic archaea, and was subsequently transferred into the bacterial domain.

The strict anaerobe Bacteroides fragilis grows in and benefits from nanomolar concentrations of oxygen

Strict anaerobes cannot grow in the presence of greater than 5 micro M dissolved oxygen. Despite this growth inhibition, many strict anaerobes of the Bacteroides class of eubacteria can survive in oxygenated environments until the partial pressure of O2 (PO2) is sufficiently reduced. For example, the periodontal pathogens Porphyromonas gingivalis and Tannerella forsythensis colonize subgingival plaques of mammals, whereas several other Bacteroides species colonize the gastrointestinal tract of animals. It has been suggested that pre-colonization of these sites by facultative anaerobes is essential for reduction of the PO2 and subsequent colonization by strict anaerobes. However, this model is inconsistent with the observation that Bacteroides fragilis can colonize the colon in the absence of facultative anaerobes. Thus, this strict anaerobe may have a role in reduction of the environmental PO2. Although some strictly anaerobic bacteria can consume oxygen through an integral membrane electron transport system, the physiological role of this system has not been established in these organisms. Here we demonstrate that B. fragilis encodes a cytochrome bd oxidase that is essential for O2 consumption and is required, under some conditions, for the stimulation of growth in the presence of nanomolar concentrations of O2. Furthermore, our data suggest that this property is conserved in many other organisms that have been described as strict anaerobes.

Bacterial diversity and sulfur cycling in a mesophilic sulfide-rich spring

An artesian sulfide- and sulfur-rich spring in southwestern Oklahoma is shown to sustain an extremely rich and diverse microbial community. Laboratory incubations and autoradiography studies indicated that active sulfur cycling is occurring in the abundant microbial mats at Zodletone spring. Anoxygenic phototrophic bacteria oxidize sulfide to sulfate, which is reduced by sulfate-reducing bacterial populations. The microbial community at Zodletone spring was analyzed by cloning and sequencing 16S rRNA genes. A large fraction (83%) of the microbial mat clones belong to sulfur- and sulfate-reducing lineages within delta-Proteobacteria, purple sulfur gamma-Proteobacteria, epsilon -Proteobacteria, Chloroflexi, and filamentous Cyanobacteria of the order Oscillatoria as well as a novel group within gamma-Proteobacteria. The 16S clone library constructed from hydrocarbon-exposed sediments at the source of the spring had a higher diversity than the mat clone library (Shannon-Weiner index of 3.84 compared to 2.95 for the mat), with a higher percentage of clones belonging to nonphototrophic lineages (e.g., Cytophaga, Spirochaetes, Planctomycetes, Firmicutes, and Verrucomicrobiae). Many of these clones were closely related to clones retrieved from hydrocarbon-contaminated environments and anaerobic hydrocarbon-degrading enrichments. In addition, 18 of the source clones did not cluster with any of the previously described microbial divisions. These 18 clones, together with previously published or database-deposited related sequences retrieved from a wide variety of environments, could be clustered into at least four novel candidate divisions. The sulfate-reducing community at Zodletone spring was characterized by cloning and sequencing a 1.9-kb fragment of the dissimilatory sulfite reductase (DSR) gene. DSR clones belonged to the Desulfococcus-Desulfosarcina-Desulfonema group, Desulfobacter group, and Desulfovibrio group as well as to a deeply branched group in the DSR tree with no representatives from cultures. Overall, this work expands the division-level diversity of the bacterial domain and highlights the complexity of microbial communities involved in sulfur cycling in mesophilic microbial mats.

Astrobiology, the transcendent science: the promise of astrobiology as an integrative approach for science and engineering education and research

Astrobiology is rapidly gaining the worldwide attention of scientists, engineers and the public. Astrobiology's captivation is due to its inherently interesting focus on life, its origins and distribution in the Universe. Because of its remarkable breadth as a scientific field, astrobiology touches on virtually all disciplines in the physical, biological and social sciences as well as engineering. The multidisciplinary nature and the appeal of its subject matter make astrobiology ideal for integrating the teaching of science at all levels in educational curricula. The rationale for implementing novel educational programs in astrobiology is presented along with specific research and educational policy recommendations.

The interface between the biological and inorganic worlds: iron-sulfur metalloclusters

Complex iron-sulfur metalloclusters form the active sites of the enzymes that catalyze redox transformations of N2, CO, and H2, which are likely components of Earth's primordial atmosphere. Although these centers reflect the organizational principles of simpler iron-sulfur clusters, they exhibit extensive elaborations that confer specific ligand-binding and catalytic properties. These changes were probably achieved through evolutionary processes, including the fusion of small clusters, the addition of new metals, and the development of cluster assembly pathways, driven by selective pressures resulting from changes in the chemical composition of the biosphere.

Mitochondrial gene history and mRNA localization: is there a correlation?

Phylogenetic studies of the yeast mitochondrial proteome have shown a complex evolutionary scenario, in which proteins of bacterial origin form complexes with proteins of eukaryotic origin. Exciting new results from whole-genome microarray studies of subcellular mRNA localizations have shown that mRNAs that are of putative bacterial origin are mainly translated on polysomes that are associated with the mitochondrion, whereas those of eukaryotic origin are generally translated on free cytosolic polysomes. Understanding these newly discovered relationships promises insights into old questions about organelle origins and mRNA localization in the eukaryotic cell.

Nitrogen fixation and photosynthetic oxygen evolution in cyanobacteria

The biological reduction of N(2) is catalyzed by nitrogenase, which is irreversibly inhibited by molecular oxygen. Cyanobacteria are the only diazotrophs (nitrogen-fixing organisms) that produce oxygen as a by-product of the photosynthetic process, and which must negotiate the inevitable presence of molecular oxygen with an essentially anaerobic enzyme. In this review, we present an analysis of the geochemical conditions under which nitrogenase evolved and examine how the evolutionary history of the enzyme complex corresponds to the physiological, morphological, and developmental strategies for reducing damage by molecular oxygen. Our review highlights biogeochemical constraints on diazotrophic cyanobacteria in the contemporary world.

Ozone concentrations and ultraviolet fluxes on Earth-like planets around other stars

Coupled radiative-convective/photochemical modeling was performed for Earth-like planets orbiting different types of stars (the Sun as a G2V, an F2V, and a K2V star). O(2) concentrations between 1 and 10(-5) times the present atmospheric level (PAL) were simulated. The results were used to calculate visible/near-IR and thermal-IR spectra, along with surface UV fluxes and relative dose rates for erythema and DNA damage. For the spectral resolution and sensitivity currently planned for the first generation of terrestrial planet detection and characterization missions, we find that O(2) should be observable remotely in the visible for atmospheres containing at least 10(-2) PAL of O(2). O(3) should be visible in the thermal-IR for atmospheres containing at least 10(-3) PAL of O(2). CH(4) is not expected to be observable in 1 PAL O(2) atmospheres like that of modern Earth, but it might be observable at thermal-IR wavelengths in "mid-Proterozoic-type" atmospheres containing approximately 10(-1) PAL of O(2). Thus, the simultaneous detection of both O(3) and CH(4) - considered to be a reliable indication of life - is within the realm of possibility. High-O(2) planets orbiting K2V and F2V stars are both better protected from surface UV radiation than is modern Earth. For the F2V case the high intrinsic UV luminosity of the star is more than offset by the much thicker ozone layer. At O(2) levels below approximately 10(-2) PAL, planets around all three types of stars are subject to high surface UV fluxes, with the F2V planet exhibiting the most biologically dangerous radiation environment. Thus, while advanced life is theoretically possible on high-O(2) planets around F stars, it is not obvious that it would evolve as it did on Earth.

Life and the evolution of Earth's atmosphere

Harvesting light to produce energy and oxygen (photosynthesis) is the signature of all land plants. This ability was co-opted from a precocious and ancient form of life known as cyanobacteria. Today these bacteria, as well as microscopic algae, supply oxygen to the atmosphere and churn out fixed nitrogen in Earth's vast oceans. Microorganisms may also have played a major role in atmosphere evolution before the rise of oxygen. Under the more dim light of a young sun cooler than today's, certain groups of anaerobic bacteria may have been pumping out large amounts of methane, thereby keeping the early climate warm and inviting. The evolution of Earth's atmosphere is linked tightly to the evolution of its biota.

Questioning the evidence for Earth's oldest fossils

Structures resembling remarkably preserved bacterial and cyanobacterial microfossils from about 3,465-million-year-old Apex cherts of the Warrawoona Group in Western Australia currently provide the oldest morphological evidence for life on Earth and have been taken to support an early beginning for oxygen-producing photosynthesis. Eleven species of filamentous prokaryote, distinguished by shape and geometry, have been put forward as meeting the criteria required of authentic Archaean microfossils, and contrast with other microfossils dismissed as either unreliable or unreproducible. These structures are nearly a billion years older than putative cyanobacterial biomarkers, genomic arguments for cyanobacteria, an oxygenic atmosphere and any comparably diverse suite of microfossils. Here we report new research on the type and re-collected material, involving mapping, optical and electron microscopy, digital image analysis, micro-Raman spectroscopy and other geochemical techniques. We reinterpret the purported microfossil-like structure as secondary artefacts formed from amorphous graphite within multiple generations of metalliferous hydrothermal vein chert and volcanic glass. Although there is no support for primary biological morphology, a Fischer--Tropsch-type synthesis of carbon compounds and carbon isotopic fractionation is inferred for one of the oldest known hydrothermal systems on Earth.

Mass-independent fractionation of sulfur isotopes in Archean sediments: strong evidence for an anoxic Archean atmosphere

Mass-independent fractionation (MIF) of sulfur isotopes has been reported in sediments of Archean and Early Proterozoic Age (> 2.3 Ga) but not in younger rocks. The only fractionation mechanism that is consistent with the data on all four sulfur isotopes involves atmospheric photochemical reactions such as SO2 photolysis. We have used a one-dimensional photochemical model to investigate how the isotopic fractionation produced during SO2 photolysis would have been transferred to other gaseous and particulate sulfur-bearing species in both low-O2 and high-O2 atmospheres. We show that in atmospheres with O2 concentrations < 10(-5) times the present atmospheric level (PAL), sulfur would have been removed from the atmosphere in a variety of different oxidation states, each of which would have had its own distinct isotopic signature. By contrast, in atmospheres with O2 concentrations > or = 10(-5) PAL, all sulfur-bearing species would have passed through the oceanic sulfate reservoir before being incorporated into sediments, so any signature of MIF would have been lost. We conclude that the atmospheric O2 concentration must have been < 10(-5) PAL prior to 2.3 Ga.

Carbon dioxide cycling through the mantle and implications for the climate of ancient Earth

The continental cycle of silicate weathering and metamorphism dynamically buffers atmospheric CO2 and climate. Feedback is provided by the temperature dependence of silicate weathering. Here we argue that hydrothermal alteration of oceanic basalts also dynamically buffers CO2. The oceanic cycle is linked to the mantle via subduction of carbonatized basalts and degassing of CO2 at the mid-ocean ridges. Feedback is provided by the dependence of carbonatization on the amount of dissolved carbonate in sea water. Unlike the continental cycle, the oceanic cycle has no thermostat. Hence surface temperatures can become very low if CO2 is the only greenhouse gas apart from water. Currently the continental cycle is more important, but early in Earth’s history the oceanic cycle was probably dominant. We argue that CO2 greenhouses thick enough to defeat the faint early Sun are implausible and that, if no other greenhouse gases are invoked, very cold climates are expected for much of Proterozoic and Archaean time. We echo current fashion and favour biogenic methane as the chief supplement to CO2. Fast weathering and probable subduction of abundant impact ejecta would have reduced CO2 levels still further in Hadean time. Despite its name, the Hadean Eon might have been the coldest era in the history of the Earth.