Geological constraints on the origin of oxygenic photosynthesis

Dating Ammonia-Oxidizing Bacteria with Abundant Eukaryotic Fossils

Evolution of a complete nitrogen (N) cycle relies on the onset of ammonia oxidation, which aerobically converts ammonia to nitrogen oxides. However, accurate estimation of the antiquity of ammonia-oxidizing bacteria (AOB) remains challenging because AOB-specific fossils are absent and bacterial fossils amenable to calibrate molecular clocks are rare. Leveraging the ancient endosymbiosis of mitochondria and plastid, as well as using state-of-the-art Bayesian sequential dating approach, we obtained a timeline of AOB evolution calibrated largely by eukaryotic fossils. We show that the first AOB evolved in marine Gammaproteobacteria (Gamma-AOB) and emerged between 2.1 and 1.9 billion years ago (Ga), thus postdating the Great Oxidation Event (GOE; 2.4 to 2.32 Ga). To reconcile the sedimentary N isotopic signatures of ammonia oxidation occurring near the GOE, we propose that ammonia oxidation likely occurred at the common ancestor of Gamma-AOB and Gammaproteobacterial methanotrophs, or the actinobacterial/verrucomicrobial methanotrophs which are known to have ammonia oxidation activities. It is also likely that nitrite was transported from the terrestrial habitats where ammonia oxidation by archaea took place. Further, we show that the Gamma-AOB predated the anaerobic ammonia-oxidizing (anammox) bacteria, implying that the emergence of anammox was constrained by the availability of dedicated ammonia oxidizers which produce nitrite to fuel anammox. Our work supports a new hypothesis that N redox cycle involving nitrogen oxides evolved rather late in the ocean.

Chapter 6: The Breadth and Limits of Life on Earth

Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.

Loss of plastid ndh genes in an autotrophic desert plant

Plant plastid genomes are highly conserved with most flowering plants having the same complement of essential plastid genes. Here, we report the loss of five of the eleven NADH dehydrogenase subunit genes (ndh) in the plastid of a desert plant jojoba (Simmondsia chinensis). The plastid genome of jojoba was 156,496 bp with one large single copy region (LSC), a very small single copy region (SSC) and two expanded inverted repeats (IRA + IRB). The NADH dehydrogenase (NDH) complex is comprised of several protein subunits, encoded by the ndh genes of the plastome and the nucleus. The ndh genes are critical to the proper functioning of the photosynthetic electron transport chain and protection of plants from oxidative stress. Most plants are known to contain all eleven ndh genes. Plants with missing or defective ndh genes are often heterotrophs either due to their complete or holo- or myco- parasitic nature. Plants with a defective NDH complex, caused by the deletion/pseudogenisation of some or all the ndh genes, survive in milder climates suggesting the likely extinction of plant lineages lacking these genes under harsh climates. Interestingly, some autotrophic plants do exist without ndh gene/s and can cope with high or low light. This implies that these plants are protected from oxidative stress by mechanisms excluding ndh genes. Jojoba has evolved mechanisms to cope with a non-functioning NDH complex and survives in extreme desert conditions with abundant sunlight and limited water.

Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria

Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].

Solar energy conversion by photosystem II: principles and structures

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

Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms

Viral infections modulate bacterial metabolism and ecology. Here, we investigated the hypothesis that viruses influence the ecology of purple and green sulfur bacteria in anoxic and sulfidic lakes, analogs of euxinic oceans in the geologic past. By screening metagenomes from lake sediments and water column, in addition to publicly-available genomes of cultured purple and green sulfur bacteria, we identified almost 300 high and medium-quality viral genomes. Viruses carrying the gene psbA, encoding the small subunit of photosystem II protein D1, were ubiquitous, suggesting viral interference with the light reactions of sulfur oxidizing autotrophs. Viruses predicted to infect these autotrophs also encoded auxiliary metabolic genes for reductive sulfur assimilation as cysteine, pigment production, and carbon fixation. These observations show that viruses have the genomic potential to modulate the production of metabolic markers of phototrophic sulfur bacteria that are used to identify photic zone euxinia in the geologic past.

Three Parts of the Plant Genome: On the Way to Success in the Production of Recombinant Proteins

Recombinant proteins are the most important product of current industrial biotechnology. They are indispensable in medicine (for diagnostics and treatment), food and chemical industries, and research. Plant cells combine advantages of the eukaryotic protein production system with simplicity and efficacy of the bacterial one. The use of plants for the production of recombinant proteins is an economically important and promising area that has emerged as an alternative to traditional approaches. This review discusses advantages of plant systems for the expression of recombinant proteins using nuclear, plastid, and mitochondrial genomes. Possibilities, problems, and prospects of modifications of the three parts of the genome in light of obtaining producer plants are examined. Examples of successful use of the nuclear expression platform for production of various biopharmaceuticals, veterinary drugs, and technologically important proteins are described, as are examples of a high yield of recombinant proteins upon modification of the chloroplast genome. Potential utility of plant mitochondria as an expression system for the production of recombinant proteins and its advantages over the nucleus and chloroplasts are substantiated. Although these opportunities have not yet been exploited, potential utility of plant mitochondria as an expression system for the production of recombinant proteins and its advantages over the nucleus and chloroplasts are substantiated.

Bulk and grain-scale minor sulfur isotope data reveal complexities in the dynamics of Earth's oxygenation

The permanent disappearance of mass-independent sulfur isotope fractionation (S-MIF) from the sedimentary record has become a widely accepted proxy for atmospheric oxygenation. This framework, however, neglects inheritance from oxidative weathering of pre-existing S-MIF–bearing sedimentary sulfide minerals (i.e., crustal memory), which has recently been invoked to explain apparent discrepancies within the sulfur isotope record. Herein, we demonstrate that such a crustal memory effect does not confound the Carletonville S-isotope record; rather, the pronounced Δ³³S values identified within the Rooihoogte Formation represent the youngest known unequivocal oxygen-free photochemical products. Previously observed ³³S-enrichments within the succeeding Timeball Hill Formation, however, contrasts with our record, revealing kilometer-scale heterogeneities that highlight significant uncertainties in our understanding of the dynamics of Earth’s oxygenation.

The disappearance of mass-independent sulfur isotope fractionation (S-MIF) within the c. 2.3-billion-year-old (Ga) Rooihoogte Formation has been heralded as a chemostratigraphic marker of permanent atmospheric oxygenation. Reports of younger S-MIF, however, question this narrative, leaving significant uncertainties surrounding the timing, tempo, and trajectory of Earth’s oxygenation. Leveraging a new bulk quadruple S-isotope record, we return to the South African Transvaal Basin in search of support for supposed oscillations in atmospheric oxygen beyond 2.3 Ga. Here, as expected, within the Rooihoogte Formation, our data capture a collapse in Δ^3×S values and a shift from Archean-like Δ³⁶S/Δ³³S slopes to their mass-dependent counterparts. Importantly, the interrogation of a Δ³³S-exotic grain reveals extreme spatial variability, whereby atypically large Δ³³S values are separated from more typical Paleoproterozoic values by a subtle grain-housed siderophile-enriched band. This isotopic juxtaposition signals the coexistence of two sulfur pools that were able to escape diagenetic homogenization. These large Δ³³S values require an active photochemical sulfur source, fingerprinting atmospheric S-MIF production after its documented cessation elsewhere at ∼2.4 Ga. By contrast, the Δ³³S monotony observed in overlying Timeball Hill Formation, with muted Δ³³S values (<0.3‰) and predominantly mass-dependent Δ³⁶S/Δ³³S systematics, remains in stark contrast to recent reports of pronounced S-MIF within proximal formational equivalents. If reflective of atmospheric processes, these observed kilometer-scale discrepancies disclose heterogenous S-MIF delivery to the Transvaal Basin and/or poorly resolved fleeting returns to S-MIF production. Rigorous bulk and grain-scale analytical campaigns remain paramount to refine our understanding of Earth’s oxygenation and substantiate claims of post-2.3 Ga oscillations in atmospheric oxygen.

Processing of D1 Protein: A Mysterious Process Carried Out in Thylakoid Lumen

In oxygenic photosynthetic organisms, D1 protein, a core subunit of photosystem II (PSII), displays a rapid turnover in the light, in which D1 proteins are distinctively damaged and immediately removed from the PSII. In parallel, as a repair process, D1 proteins are synthesized and simultaneously assembled into the PSII. On this flow, the D1 protein is synthesized as a precursor with a carboxyl-terminal extension, and the D1 processing is defined as a step for proteolytic removal of the extension by a specific protease, CtpA. The D1 processing plays a crucial role in appearance of water-oxidizing capacity of PSII, because the main chain carboxyl group at carboxyl-terminus of the D1 protein, exposed by the D1 processing, ligates a manganese and a calcium atom in the Mn4CaO5-cluster, a special equipment for water-oxidizing chemistry of PSII. This review focuses on the D1 processing and discusses it from four angles: (i) Discovery of the D1 processing and recognition of its importance: (ii) Enzyme involved in the D1 processing: (iii) Efforts for understanding significance of the D1 processing: (iv) Remaining mysteries in the D1 processing. Through the review, I summarize the current status of our knowledge on and around the D1 processing.

Evidence for the oxidation of Earth's crust from the evolution of manganese minerals

Analysis of manganese mineral occurrences and valence states demonstrate oxidation of Earth's crust through time. Changes in crustal redox state are critical to Earth's evolution, but few methods exist for evaluating spatially averaged crustal redox state through time. Manganese (Mn) is a redox-sensitive metal whose variable oxidation states and abundance in crustal minerals make it a useful tracer of crustal oxidation. We find that the average oxidation state of crustal Mn occurrences has risen in the last 1 billion years in response to atmospheric oxygenation following a 66 ± 1 million-year time lag. We interpret this lag as the average time necessary to equilibrate the shallow crust to atmospheric oxygen fugacity. This study employs large mineralogical databases to evaluate geochemical conditions through Earth's history, and we propose that this and other mineral data sets form an important class of proxies that constrain the evolving redox state of various Earth reservoirs.

OUP accepted manuscript

Oxygen (O₂) is the ultimate oxidant on Earth and its respiration confers such an energetic advantage that microorganisms have evolved the capacity to scavenge O₂ down to nanomolar concentrations. The respiration of O₂ at extremely low levels is proving to be common to diverse microbial taxa, including organisms formerly considered strict anaerobes. Motivated by recent advances in O₂ sensing and DNA/RNA sequencing technologies, we performed a systematic review of environmental metatranscriptomes revealing that microbial respiration of O₂ at nanomolar concentrations is ubiquitous and drives microbial activity in seemingly anoxic aquatic habitats. These habitats were key to the early evolution of life and are projected to become more prevalent in the near future due to anthropogenic-driven environmental change. Here, we summarize our current understanding of aerobic microbial respiration under apparent anoxia, including novel processes, their underlying biochemical pathways, the involved microorganisms, and their environmental importance and evolutionary origin.

Microbial processes during deposition and diagenesis of Banded Iron Formations

Banded Iron Formations (BIFs) are marine chemical sediments consisting of alternating iron (Fe)-rich and silica (Si)-rich bands which were deposited throughout much of the Precambrian era. BIFs represent important proxies for the geochemical composition of Precambrian seawater and provide evidence for early microbial life. Iron present in BIFs was likely precipitated in the form of Fe3+ (Fe(III)) minerals, such as ferrihydrite (Fe(OH)3), either through the metabolic activity of anoxygenic photoautotrophic Fe2+ (Fe(II))-oxidizing bacteria (photoferrotrophs), by microaerophilic bacteria, or by the oxidation of dissolved Fe(II) by O2 produced by early cyanobacteria. However, in addition to oxidized Fe-bearing minerals such as hematite (FeIII 2O3), (partially) reduced minerals such as magnetite (FeIIFeIII 2O4) and siderite (FeIICO3) are found in BIFs as well. The presence of reduced Fe in BIFs has been suggested to reflect the reduction of primary Fe(III) minerals by dissimilatory Fe(III)-reducing bacteria, or by metamorphic (high pressure and temperature) reactions occurring in presence of buried organic matter. Here, we present the current understanding of the role of Fe-metabolizing bacteria in the deposition of BIFs, as well as competing hypotheses that favor an abiotic model for BIF deposition. We also discuss the potential abiotic and microbial reduction of Fe(III) in BIFs after deposition. Further, we review the availability of essential nutrients (e.g. P and Ni) and their implications on early Earth biogeochemistry. Overall, the combined results of various ancient seawater analogue experiments aimed at assessing microbial iron cycling pathways, coupled with the analysis of the BIF rock record, point towards a strong biotic influence during BIF genesis.

Diurnal Fe(II)/Fe(III) cycling and enhanced O2 production in a simulated Archean marine oxygen oasis

The oxygenation of early Earth’s atmosphere during the Great Oxidation Event, is generally accepted to have been caused by oceanic Cyanobacterial oxygenic photosynthesis. Recent studies suggest that Fe(II) toxicity delayed the Cyanobacterial expansion necessary for the GOE. This study investigates the effects of Fe(II) on two Cyanobacteria, Pseudanabaena sp. PCC7367 and Synechococcus sp. PCC7336, in a simulated shallow-water marine Archean environment. A similar Fe(II) toxicity response was observed as reported for closed batch cultures. This toxicity was not observed in cultures provided with continuous gaseous exchange that showed significantly shorter doubling times than the closed-culture system, even with repeated nocturnal addition of Fe(II) for 12 days. The green rust (GR) formed under high Fe(II) conditions, was not found to be directly toxic to Pseudanabaena sp. PCC7367. In summary, we present evidence of diurnal Fe cycling in a simulated shallow-water marine environment for two ancestral strains of Cyanobacteria, with increased O₂ production under anoxic conditions.

Cyanobacterial photosynthesis is thought to have oxygenated Earth’s atmosphere during the Great Oxidation Event, but these organisms had to overcome the toxic effects of iron. Here the authors simulate Archaean conditions in Cyanobacterial cultures and find that gas exchange and rust formation alleviated iron toxicity.

Sulfur Chemistry May Have Paved the Way for Evolution of Antioxidants

The first organisms on the young Earth, just 1-1.5 billion years old, were likely chemolithoautotrophic anaerobes, thriving in an anoxic world rich in water, CO₂, and N₂. It is generally assumed that, until the accumulation of O₂ in the atmosphere, life was exempted from the oxidative stress that reactive oxygen species (ROS) impose on hydrocarbon-based life. Therefore, it is perplexing to note that life on the early Earth already carried antioxidants such as superoxide dismutase enzymes, catalase, and peroxiredoxins, the function of which is to counteract all forms of ROS, including H₂O₂. Phylogenetic investigations suggest that the presence of these enzymes in the last universal common ancestor, far predating the great oxygenation event (GOE) sometime between 2.3 and 2.7 billion years ago, is thought to be due to the appearance of oxygen-producing microorganisms and the subsequent need to respond to the appearance of ROS. Since the metabolic enzymes that counteract ROS have been found in all domains of life, they are considered of primitive origin. Two questions arise: (1) Could there be a nonbiological source of ROS that predates the oxygenic microbial activity? (2) Could sulfur, the homologue of oxygen, have played that role? Reactive sulfur species (RSS) may have triggered the evolution of antioxidants such that the ROS antioxidants started out as "antisulfur" enzymes developed to cope with, and take advantage of, various forms of RSS that were abundantly present on the early Earth.

Evolutionary trends in RuBisCO kinetics and their co-evolution with CO2 concentrating mechanisms

RuBisCO-catalyzed CO₂ fixation is the main source of organic carbon in the biosphere. This enzyme is present in all domains of life in different forms (III, II, and I) and its origin goes back to 3500 Mya, when the atmosphere was anoxygenic. However, the RuBisCO active site also catalyzes oxygenation of ribulose 1,5-bisphosphate, therefore, the development of oxygenic photosynthesis and the subsequent oxygen-rich atmosphere promoted the appearance of CO₂ concentrating mechanisms (CCMs) and/or the evolution of a more CO₂ -specific RuBisCO enzyme. The wide variability in RuBisCO kinetic traits of extant organisms reveals a history of adaptation to the prevailing CO₂ /O₂ concentrations and the thermal environment throughout evolution. Notable differences in the kinetic parameters are found among the different forms of RuBisCO, but the differences are also associated with the presence and type of CCMs within each form, indicative of co-evolution of RuBisCO and CCMs. Trade-offs between RuBisCO kinetic traits vary among the RuBisCO forms and also among phylogenetic groups within the same form. These results suggest that different biochemical and structural constraints have operated on each type of RuBisCO during evolution, probably reflecting different environmental selective pressures. In a similar way, variations in carbon isotopic fractionation of the enzyme point to significant differences in its relationship to the CO₂ specificity among different RuBisCO forms. A deeper knowledge of the natural variability of RuBisCO catalytic traits and the chemical mechanism of RuBisCO carboxylation and oxygenation reactions raises the possibility of finding unrevealed landscapes in RuBisCO evolution.

A paleosol record of the evolution of Cr redox cycling and evidence for an increase in atmospheric oxygen during the Neoproterozoic

Atmospheric oxygen levels control the oxidative side of key biogeochemical cycles and place limits on the development of high-energy metabolisms. Understanding Earth's oxygenation is thus critical to developing a clearer picture of Earth's long-term evolution. However, there is currently vigorous debate about even basic aspects of the timing and pattern of the rise of oxygen. Chemical weathering in the terrestrial environment occurs in contact with the atmosphere, making paleosols potentially ideal archives to track the history of atmospheric O₂ levels. Here we present stable chromium isotope data from multiple paleosols that offer snapshots of Earth surface conditions over the last three billion years. The results indicate a secular shift in the oxidative capacity of Earth's surface in the Neoproterozoic and suggest low atmospheric oxygen levels (<1% PAL pO₂ ) through the majority of Earth's history. The paleosol record also shows that localized Cr oxidation may have begun as early as the Archean, but efficient, modern-like transport of hexavalent Cr under an O₂ -rich atmosphere did not become common until the Neoproterozoic.

The evolution and productivity of carbon fixation pathways in response to changes in oxygen concentration over geological time

The fixation of inorganic carbon species like CO₂ to more reduced organic forms is one of the most fundamental processes of life as we know it. Although several carbon fixation pathways are known to exist, on Earth today nearly all global carbon fixation is driven by the Calvin cycle in oxygenic photosynthetic plants, algae, and Cyanobacteria. At other times in Earth history, other organisms utilizing different carbon fixation pathways may have played relatively larger roles, with this balance shifting over geological time as the environmental context of life has changed and evolutionary innovations accumulated. Among the most dramatic changes that our planet and the biosphere have undergone are those surrounding the rise of O₂ in our atmosphere-first during the Great Oxygenation Event at ∼2.3 Ga, and perhaps again during Neoproterozoic or Paleozoic time. These oxygenation events likely represent major step changes in the tempo and mode of biological productivity as a result of the increased productivity of oxygenic photosynthesis and the introduction of O₂ into geochemical and biological systems, and likely involved shifts in the relative contribution of different carbon fixation pathways. Here, we review what is known from both the rock record and comparative biology about the evolution of carbon fixation pathways, their contributions to primary productivity through time, and their relationship to the evolving oxygenation state of the fluid Earth following the evolution and expansion of oxygenic photosynthesis.

Organic geochemical approaches to understanding early life

Here we discuss the early geological record of preserved organic carbon and the criteria that must be applied to distinguish biological from non-biological origins. Sedimentary graphite, irrespective of its isotopic composition, does not constitute a reliable biosignature because the rocks in which it is found are generally metamorphosed to the point where convincing signs of life have been erased. Rather, multiple lines of evidence, including sedimentary textures, microfossils, large accumulations of organic matter and isotopic data for co-existing carbon, nitrogen and sulfur are required before biological origin can be convincingly demonstrated.

Evolution of cellular metabolism and the rise of a globally productive biosphere

Metabolic processes in cells and chemical processes in the environment are fundamentally intertwined and have evolved in concert for most of Earth's existence. Here I argue that intrinsic properties of cellular metabolism imposed central constraints on the historical trajectories of biopsheric productivity and atmospheric oxygenation. Photosynthesis depends on iron, but iron is highly insoluble under the aerobic conditions produced by oxygenic photosynthesis. These counteracting constraints led to two major stages of Earth oxygenation. After a cyanobacteria-driven biospheric expansion near the Archean-Proterozoic boundary, productivity remained largely restricted to continental boundaries and shallow aquatic environments where weathering inputs made iron more accessible. The anoxic deep open ocean was rich in free iron during the Proterozoic, but this iron was largely inaccessible, partly because an otherwise nutrient-poor ocean was limiting to photosynthesis, but also because a photosynthetic expansion would have quenched its own iron supply. Near the Proterozoic-Phanerozoic boundary, bioenergetics innovations allowed eukaryotic photosynthesis to overcome these interconnected negative feedbacks and begin expanding into the deep open oceans and onto the continents, where nutrients are inherently harder to come by. Key insights into what drove the ecological rise of eukaryotic photosynthesis emerge from analyses of marine Synechococcus and Prochlorococcus, abundant marine picocyanobacteria whose ancestors colonized the oceans in the Neoproterozoic. The reconstructed evolution of this group reveals a sequence of innovations that ultimately produced a form of photosynthesis in Prochlorococcus that is more like that of green plant cells than other cyanobacteria. Innovations increased the energy flux of cells, thereby enhancing their ability to acquire sparse nutrients, and as by-product also increased the production of organic carbon waste. Some of these organic waste products had the ability to chelate iron and make it bioavailable, thereby indirectly pushing the oceans through a transition from an anoxic state rich in free iron to an oxygenated state with organic carbon-bound iron. Resulting conditions (and parallel processes on the continents) in turn led to a series of positive feedbacks that increased the availability of other nutrients, thereby promoting the rise of a globally productive biosphere. In addition to the occurrence of major biospheric expansions, the several hundred million-year periods around the Archean-Proterozoic and Proterozoic-Phanerozoic boundaries share a number of other parallels. Both epochs have also been linked to major carbon cycle perturbations and global glaciations, as well as changes in the nature of plate tectonics and increases in continental exposure and weathering. This suggests the dynamics of life and Earth are intimately intertwined across many levels and that general principles governed transitions in these coupled dynamics at both times in Earth history.

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.

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

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

Unusual microbial mat-related structural diversity 2.1 billion years ago and implications for the Francevillian biota

The 2.1-billion-year-old (Ga) Francevillian series in Gabon hosts some of the oldest reported macroscopic fossils of various sizes and shapes, stimulating new debates on the origin, evolution and organization of early complex life. Here, we document ten representative types of exceptionally well-preserved mat-related structures, comprising "elephant-skin" textures, putative macro-tufted microbial mats, domal buildups, flat pyritized structures, discoidal microbial colonies, horizontal mat growth patterns, wrinkle structures, "kinneyia" structures, linear patterns and nodule-like structures. A combination of petrographic analyses, scanning electron microscopy, Raman spectroscopy and organic elemental analyses of carbon-rich laminae and microtexture, indicate a biological origin for these structures. The observed microtextures encompass oriented grains, floating silt-sized quartz grains, concentrated heavy minerals, randomly oriented clays, wavy-crinkly laminae and pyritized structures. Based on comparisons with modern analogues, as well as an average δ¹³ C organic matter (C_org ) composition of -32.94 ± 1.17‰ (1 standard deviation, SD) with an outlier of -41.26‰, we argue that the mat-related structures contain relicts of multiple carbon pathways including heterotrophic recycling of photosynthetically derived C_org . Moreover, the relatively close association of the macroscopic fossil assemblages to the microbial mats may imply that microbial communities acted as potential benthic O₂ oases linked to oxyphototrophic cyanobacterial mats and grazing grounds. In addition, the mat's presence likely improved the preservation of the oldest large colonial organisms, as they are known to strongly biostabilize sediments. Our findings highlight the oldest community assemblage of microscopic and macroscopic biota in the aftermath of the "Great Oxidation Event," widening our understanding of biological organization during Earth's middle age.

Constraints on Paleoproterozoic atmospheric oxygen levels

The oxygenation of Earth's surface environment dramatically altered key biological and geochemical cycles and ultimately ushered in the rise of an ecologically diverse biosphere. However, atmospheric oxygen partial pressures (pO2) estimates for large swaths of the Precambrian remain intensely debated. Here we evaluate and explore the use of carbonate cerium (Ce) anomalies (Ce/Ce*) as a quantitative atmospheric pO2 proxy and provide estimates of Proterozoic pO2 using marine carbonates from a unique Precambrian carbonate succession-the Paleoproterozoic Pethei Group. In contrast to most previous work, we measure Ce/Ce* on marine carbonate precipitates that formed in situ across a depth gradient, building on previous detailed sedimentology and stratigraphy to constrain the paleo-depth of each sample. Measuring Ce/Ce* across a full platform to basin depth gradient, we found only minor depleted Ce anomalies restricted to the platform and upper slope facies. We combine these results with a Ce oxidation model to provide a quantitative constraint on atmospheric pO2 1.87 billion years ago (Ga). Our results suggest Paleoproterozoic atmospheric oxygen concentrations were low, near 0.1% of the present atmospheric level. This work provides another crucial line of empirical evidence that atmospheric oxygen levels returned to low concentrations following the Lomagundi Event, and remained low enough for large portions of the Proterozoic to have impacted the ecology of the earliest complex organisms.

High pCO2-induced exopolysaccharide-rich ballasted aggregates of planktonic cyanobacteria could explain Paleoproterozoic carbon burial

The contribution of planktonic cyanobacteria to burial of organic carbon in deep-sea sediments before the emergence of eukaryotic predators ~1.5 Ga has been considered negligible owing to the slow sinking speed of their small cells. However, global, highly positive excursion in carbon isotope values of inorganic carbonates ~2.22-2.06 Ga implies massive organic matter burial that had to be linked to oceanic cyanobacteria. Here to elucidate that link, we experiment with unicellular planktonic cyanobacteria acclimated to high partial CO2 pressure (pCO2) representative of the early Paleoproterozoic. We find that high pCO2 boosts generation of acidic extracellular polysaccharides (EPS) that adsorb Ca and Mg cations, support mineralization, and aggregate cells to form ballasted particles. The down flux of such self-assembled cyanobacterial aggregates would decouple the oxygenic photosynthesis from oxidative respiration at the ocean scale, drive export of organic matter from surface to deep ocean and sustain oxygenation of the planetary surface.

Genomic Changes Associated with the Evolutionary Transitions of Nostoc to a Plant Symbiont

Cyanobacteria belonging to the genus Nostoc comprise free-living strains and also facultative plant symbionts. Symbiotic strains can enter into symbiosis with taxonomically diverse range of host plants. Little is known about genomic changes associated with evolutionary transition of Nostoc from free-living to plant symbiont. Here, we compared the genomes derived from 11 symbiotic Nostoc strains isolated from different host plants and infer phylogenetic relationships between strains. Phylogenetic reconstructions of 89 Nostocales showed that symbiotic Nostoc strains with a broad host range, entering epiphytic and intracellular or extracellular endophytic interactions, form a monophyletic clade indicating a common evolutionary history. A polyphyletic origin was found for Nostoc strains which enter only extracellular symbioses, and inference of transfer events implied that this trait was likely acquired several times in the evolution of the Nostocales. Symbiotic Nostoc strains showed enriched functions in transport and metabolism of organic sulfur, chemotaxis and motility, as well as the uptake of phosphate, branched-chain amino acids, and ammonium. The genomes of the intracellular clade differ from that of other Nostoc strains, with a gain/enrichment of genes encoding proteins to generate l-methionine from sulfite and pathways for the degradation of the plant metabolites vanillin and vanillate, and of the macromolecule xylan present in plant cell walls. These compounds could function as C-sources for members of the intracellular clade. Molecular clock analysis indicated that the intracellular clade emerged ca. 600 Ma, suggesting that intracellular Nostoc symbioses predate the origin of land plants and the emergence of their extant hosts.

Searching for the Great Oxidation Event in North America: A Reappraisal of the Huronian Supergroup by SIMS Sulfur Four-Isotope Analysis

Sedimentological observations from the Paleoproterozoic Huronian Supergroup are suggested to mark the rise in atmospheric oxygen at that time, which is commonly known as the Great Oxidation Event (GOE) and typically coupled with a transition from mass-independent fractionation (MIF) to mass-dependent fractionation (MDF) of sulfur isotopes. An early in situ study of S three-isotopes across the Huronian Supergroup by Papineau et al. ( 2007 ) identified a weak MIF-MDF transition. However, the interpretation and stratigraphic placement of this transition is ambiguous. In this study, all four S isotopes were analyzed for the first time in two Huronian drill cores by secondary ion mass spectrometer (SIMS), and both Δ³³S and Δ³⁶S were calculated. Based on improved precision and detailed petrography, we reinterpret the dominance of pyrrhotite in the studied sections, which was previously proposed as "early authigenic" in origin, as resulting from regional metamorphism. Small but analytically resolvable nonzero values of Δ³³S (from -0.07‰ to +0.38‰) and Δ³⁶S (from -4.1‰ to +1.0‰) persist throughout the lower Huronian Supergroup. Neither pronounced MIF-S signals nor a MIF-MDF transition are seen in this study. Four scenarios are proposed for the genesis of small nonzero Δ³³S and Δ³⁶S values in the Huronian: homogenization by regional metamorphism, recycling from older pyrite, dilution by magmatic fluids, and the occurrence of MDF. We argue that the precise location of the MIF-MDF transition in the Huronian remains unsolved. This putative transition may have been erased by postdepositional processes in the lower Huronian Supergroup, or may be located in the upper Huronian Supergroup. Our study highlights the importance of integrated scanning electron microscopy and secondary ion mass spectrometry techniques in deep-time studies and suggests that different analytical methods (bulk vs. SIMS) and diagenetic history (primary vs. metamorphic) among different basins may have caused inconsistent interpretations of S isotope profiles of the GOE successions at a global scale. Key Words: Great Oxidation Event (GOE)-Secondary ion mass spectrometer (SIMS)-Paleoproterozoic-Sulfur isotopes-Mass independent fractionation (MIF). Astrobiology 18, 519-538.

Life: the first two billion years

Microfossils, stromatolites, preserved lipids and biologically informative isotopic ratios provide a substantial record of bacterial diversity and biogeochemical cycles in Proterozoic (2500-541 Ma) oceans that can be interpreted, at least broadly, in terms of present-day organisms and metabolic processes. Archean (more than 2500 Ma) sedimentary rocks add at least a billion years to the recorded history of life, with sedimentological and biogeochemical evidence for life at 3500 Ma, and possibly earlier; phylogenetic and functional details, however, are limited. Geochemistry provides a major constraint on early evolution, indicating that the first bacteria were shaped by anoxic environments, with distinct patterns of major and micronutrient availability. Archean rocks appear to record the Earth's first iron age, with reduced Fe as the principal electron donor for photosynthesis, oxidized Fe the most abundant terminal electron acceptor for respiration, and Fe a key cofactor in proteins. With the permanent oxygenation of the atmosphere and surface ocean ca 2400 Ma, photic zone O2 limited the access of photosynthetic bacteria to electron donors other than water, while expanding the inventory of oxidants available for respiration and chemoautotrophy. Thus, halfway through Earth history, the microbial underpinnings of modern marine ecosystems began to take shape.This article is part of the themed issue 'The new bacteriology'.

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

Ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components. Here, we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that there were distinct periods of amino acid substitution enrichment above background levels near and within its oxygen-sensitive active site and subunit interfaces over the divergence between Form III (associated with anoxia) and Form I (associated with oxia) groups in its evolutionary history. One possible interpretation is that these periods of substitutional enrichment are coincident with oxidative stress exerted by the rise of oxygenic photosynthesis in the Precambrian era. Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anaerobic Form III to aerobic Form I ancestral sequences predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem-bearing, oxygen-evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen-sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.

Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations

Reactive Fe(III) minerals can influence methane (CH4 ) emissions by inhibiting microbial methanogenesis or by stimulating anaerobic CH4 oxidation. The balance between Fe(III) reduction, methanogenesis, and CH4 oxidation in ferruginous Archean and Paleoproterozoic oceans would have controlled CH4 fluxes to the atmosphere, thereby regulating the capacity for CH4 to warm the early Earth under the Faint Young Sun. We studied CH4 and Fe cycling in anoxic incubations of ferruginous sediment from the ancient ocean analogue Lake Matano, Indonesia, over three successive transfers (500 days in total). Iron reduction, methanogenesis, CH4 oxidation, and microbial taxonomy were monitored in treatments amended with ferrihydrite or goethite. After three dilutions, Fe(III) reduction persisted only in bottles with ferrihydrite. Enhanced CH4 production was observed in the presence of goethite, highlighting the potential for reactive Fe(III) oxides to inhibit methanogenesis. Supplementing the media with hydrogen, nickel and selenium did not stimulate methanogenesis. There was limited evidence for Fe(III)-dependent CH4 oxidation, although some incubations displayed CH4 -stimulated Fe(III) reduction. 16S rRNA profiles continuously changed over the course of enrichment, with ultimate dominance of unclassified members of the order Desulfuromonadales in all treatments. Microbial diversity decreased markedly over the course of incubation, with subtle differences between ferrihydrite and goethite amendments. These results suggest that Fe(III) oxide mineralogy and availability of electron donors could have led to spatial separation of Fe(III)-reducing and methanogenic microbial communities in ferruginous marine sediments, potentially explaining the persistence of CH4 as a greenhouse gas throughout the first half of Earth history.

The geobiological nitrogen cycle: From microbes to the mantle

Nitrogen forms an integral part of the main building blocks of life, including DNA, RNA, and proteins. N₂ is the dominant gas in Earth's atmosphere, and nitrogen is stored in all of Earth's geological reservoirs, including the crust, the mantle, and the core. As such, nitrogen geochemistry is fundamental to the evolution of planet Earth and the life it supports. Despite the importance of nitrogen in the Earth system, large gaps remain in our knowledge of how the surface and deep nitrogen cycles have evolved over geologic time. Here, we discuss the current understanding (or lack thereof) for how the unique interaction of biological innovation, geodynamics, and mantle petrology has acted to regulate Earth's nitrogen cycle over geologic timescales. In particular, we explore how temporal variations in the external (biosphere and atmosphere) and internal (crust and mantle) nitrogen cycles could have regulated atmospheric pN₂ . We consider three potential scenarios for the evolution of the geobiological nitrogen cycle over Earth's history: two in which atmospheric pN₂ has changed unidirectionally (increased or decreased) over geologic time and one in which pN₂ could have taken a dramatic deflection following the Great Oxidation Event. It is impossible to discriminate between these scenarios with the currently available models and datasets. However, we are optimistic that this problem can be solved, following a sustained, open-minded, and multidisciplinary effort between surface and deep Earth communities.

A theory of atmospheric oxygen

Geological records of atmospheric oxygen suggest that pO₂ was less than 0.001% of present atmospheric levels (PAL) during the Archean, increasing abruptly to a Proterozoic value between 0.1% and 10% PAL, and rising quickly to modern levels in the Phanerozoic. Using a simple model of the biogeochemical cycles of carbon, oxygen, sulfur, hydrogen, iron, and phosphorous, we demonstrate that there are three stable states for atmospheric oxygen, roughly corresponding to levels observed in the geological record. These stable states arise from a series of specific positive and negative feedbacks, requiring a large geochemical perturbation to the redox state to transition from one to another. In particular, we show that a very low oxygen level in the Archean (i.e., 10^-7 PAL) is consistent with the presence of oxygenic photosynthesis and a robust organic carbon cycle. We show that the Snowball Earth glaciations, which immediately precede both transitions, provide an appropriate transient increase in atmospheric oxygen to drive the atmosphere either from its Archean state to its Proterozoic state, or from its Proterozoic state to its Phanerozoic state. This hypothesis provides a mechanistic explanation for the apparent synchronicity of the Proterozoic Snowball Earth events with both the Great Oxidation Event, and the Neoproterozoic oxidation.

Biological regulation of atmospheric chemistry en route to planetary oxygenation

Emerging evidence suggests that atmospheric oxygen may have varied before rising irreversibly ∼2.4 billion years ago, during the Great Oxidation Event (GOE). Significantly, however, pre-GOE atmospheric aberrations toward more reducing conditions-featuring a methane-derived organic-haze-have recently been suggested, yet their occurrence, causes, and significance remain underexplored. To examine the role of haze formation in Earth's history, we targeted an episode of inferred haze development. Our redox-controlled (Fe-speciation) carbon- and sulfur-isotope record reveals sustained systematic stratigraphic covariance, precluding nonatmospheric explanations. Photochemical models corroborate this inference, showing Δ³⁶S/Δ³³S ratios are sensitive to the presence of haze. Exploiting existing age constraints, we estimate that organic haze developed rapidly, stabilizing within ∼0.3 ± 0.1 million years (Myr), and persisted for upward of ∼1.4 ± 0.4 Myr. Given these temporal constraints, and the elevated atmospheric CO₂ concentrations in the Archean, the sustained methane fluxes necessary for haze formation can only be reconciled with a biological source. Correlative δ¹³C_Org and total organic carbon measurements support the interpretation that atmospheric haze was a transient response of the biosphere to increased nutrient availability, with methane fluxes controlled by the relative availability of organic carbon and sulfate. Elevated atmospheric methane concentrations during haze episodes would have expedited planetary hydrogen loss, with a single episode of haze development providing up to 2.6-18 × 10¹⁸ moles of O₂ equivalents to the Earth system. Our findings suggest the Neoarchean likely represented a unique state of the Earth system where haze development played a pivotal role in planetary oxidation, hastening the contingent biological innovations that followed.

The Architecture of Thiol Antioxidant Systems among Invertebrate Parasites

The use of oxygen as the final electron acceptor in aerobic organisms results in an improvement in the energy metabolism. However, as a byproduct of the aerobic metabolism, reactive oxygen species are produced, leaving to the potential risk of an oxidative stress. To contend with such harmful compounds, living organisms have evolved antioxidant strategies. In this sense, the thiol-dependent antioxidant defense systems play a central role. In all cases, cysteine constitutes the major building block on which such systems are constructed, being present in redox substrates such as glutathione, thioredoxin, and trypanothione, as well as at the catalytic site of a variety of reductases and peroxidases. In some cases, the related selenocysteine was incorporated at selected proteins. In invertebrate parasites, antioxidant systems have evolved in a diversity of both substrates and enzymes, representing a potential area in the design of anti-parasite strategies. The present review focus on the organization of the thiol-based antioxidant systems in invertebrate parasites. Differences between these taxa and its final mammal host is stressed. An understanding of the antioxidant defense mechanisms in this kind of parasites, as well as their interactions with the specific host is crucial in the design of drugs targeting these organisms.

Onset of the aerobic nitrogen cycle during the Great Oxidation Event

The rise of oxygen on the early Earth (about 2.4 billion years ago) caused a reorganization of marine nutrient cycles, including that of nitrogen, which is important for controlling global primary productivity. However, current geochemical records lack the temporal resolution to address the nature and timing of the biogeochemical response to oxygenation directly. Here we couple records of ocean redox chemistry with nitrogen isotope (¹⁵N/¹⁴N) values from approximately 2.31-billion-year-old shales of the Rooihoogte and Timeball Hill formations in South Africa, deposited during the early stages of the first rise in atmospheric oxygen on the Earth (the Great Oxidation Event). Our data fill a gap of about 400 million years in the temporal ¹⁵N/¹⁴N record and provide evidence for the emergence of a pervasive aerobic marine nitrogen cycle. The interpretation of our nitrogen isotope data in the context of iron speciation and carbon isotope data suggests biogeochemical cycling across a dynamic redox boundary, with primary productivity fuelled by chemoautotrophic production and a nitrogen cycle dominated by nitrogen loss processes using newly available marine oxidants. This chemostratigraphic trend constrains the onset of widespread nitrate availability associated with ocean oxygenation. The rise of marine nitrate could have allowed for the rapid diversification and proliferation of nitrate-using cyanobacteria and, potentially, eukaryotic phytoplankton.

Chromium geochemistry of the ca. 1.85 Ga Flin Flon paleosol

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

Oxygen produced by cyanobacteria in simulated Archaean conditions partly oxidizes ferrous iron but mostly escapes-conclusions about early evolution

The Earth has had a permanently oxic atmosphere only since the great oxygenation event (GOE) 2.3-2.4 billion years ago but recent geochemical research has revealed short periods of oxygen in the atmosphere up to a billion years earlier before the permanent oxygenation. If these "whiffs" of oxygen truly occurred, then oxygen-evolving (proto)cyanobacteria must have existed throughout the Archaean aeon. Trapping of oxygen by ferrous iron and other reduced substances present in Archaean oceans has often been suggested to explain why the oxygen content of the atmosphere remained negligible before the GOE although cyanobacteria produced oxygen. We tested this hypothesis by growing cyanobacteria in anaerobic high-CO₂ atmosphere in a medium with a high concentration of ferrous iron. Microcystins are known to chelate iron, which prompted us also to test the effects of microcystins and nodularins on iron tolerance. The results show that all tested cyanobacteria, especially nitrogen-fixing species grown in the absence of nitrate, and irrespective of the ability to produce cyanotoxins, were iron sensitive in aerobic conditions but tolerated high concentrations of iron in anaerobicity. This result suggests that current cyanobacteria would have tolerated the high-iron content of Archaean oceans. However, only 1 % of the oxygen produced by the cyanobacterial culture was trapped by iron, suggesting that large-scale cyanobacterial photosynthesis would have oxygenated the atmosphere even if cyanobacteria grew in a reducing ocean. Recent genomic analysis suggesting that ability to colonize seawater is a secondary trait in cyanobacteria may offer a partial explanation for the sustained inefficiency of cyanobacterial photosynthesis during the Archaean aeon, as fresh water has always covered a very small fraction of the Earth's surface. If oxygenic photosynthesis originated in fresh water, then the GOE marks the adaptation of cyanobacteria to seawater, and the late-Proterozoic increase in oxygen concentration of the atmosphere is caused by full oxidation of the oceans.

Photosynthetic Versatility in the Genome of Geitlerinema sp. PCC 9228 (Formerly Oscillatoria limnetica 'Solar Lake'), a Model Anoxygenic Photosynthetic Cyanobacterium

Anoxygenic cyanobacteria that use sulfide as the electron donor for photosynthesis are a potentially influential but poorly constrained force on Earth's biogeochemistry. Their versatile metabolism may have boosted primary production and nitrogen cycling in euxinic coastal margins in the Proterozoic. In addition, they represent a biological mechanism for limiting the accumulation of atmospheric oxygen, especially before the Great Oxidation Event and in the low-oxygen conditions of the Proterozoic. In this study, we describe the draft genome sequence of Geitlerinema sp. PCC 9228, formerly Oscillatoria limnetica 'Solar Lake', a mat-forming diazotrophic cyanobacterium that can switch between oxygenic photosynthesis and sulfide-based anoxygenic photosynthesis (AP). Geitlerinema possesses three variants of psbA, which encodes protein D1, a core component of the photosystem II reaction center. Phylogenetic analyses indicate that one variant is closely affiliated with cyanobacterial psbA genes that code for a D1 protein used for oxygen-sensitive processes. Another version is phylogenetically similar to cyanobacterial psbA genes that encode D1 proteins used under microaerobic conditions, and the third variant may be cued to high light and/or elevated oxygen concentrations. Geitlerinema has the canonical gene for sulfide quinone reductase (SQR) used in cyanobacterial AP and a putative transcriptional regulatory gene in the same operon. Another operon with a second, distinct sqr and regulatory gene is present, and is phylogenetically related to sqr genes used for high sulfide concentrations. The genome has a comprehensive nif gene suite for nitrogen fixation, supporting previous observations of nitrogenase activity. Geitlerinema possesses a bidirectional hydrogenase rather than the uptake hydrogenase typically used by cyanobacteria in diazotrophy. Overall, the genome sequence of Geitlerinema sp. PCC 9228 highlights potential cyanobacterial strategies to cope with fluctuating redox gradients and nitrogen availability that occur in benthic mats over a diel cycle. Such dynamic geochemical conditions likely also challenged Proterozoic cyanobacteria, modulating oxygen production. The genetic repertoire that underpins flexible oxygenic/anoxygenic photosynthesis in cyanobacteria provides a foundation to explore the regulation, evolutionary context, and biogeochemical implications of these co-occurring metabolisms in Earth history.

A Comprehensive Study of Cyanobacterial Morphological and Ecological Evolutionary Dynamics through Deep Geologic Time

Cyanobacteria have exerted a profound influence on the progressive oxygenation of Earth. As a complementary approach to examining the geologic record—phylogenomic and trait evolutionary analyses of extant species can lead to new insights. We constructed new phylogenomic trees and analyzed phenotypic trait data using novel phylogenetic comparative methods. We elucidated the dynamics of trait evolution in Cyanobacteria over billion-year timescales, and provide evidence that major geologic events in early Earth’s history have shaped—and been shaped by—evolution in Cyanobacteria. We identify a robust core cyanobacterial phylogeny and a smaller set of taxa that exhibit long-branch attraction artifacts. We estimated the age of nodes and reconstruct the ancestral character states of 43 phenotypic characters. We find high levels of phylogenetic signal for nearly all traits, indicating the phylogeny carries substantial predictive power. The earliest cyanobacterial lineages likely lived in freshwater habitats, had small cell diameters, were benthic or sessile, and possibly epilithic/endolithic with a sheath. We jointly analyzed a subset of 25 binary traits to determine whether rates of trait evolution have shifted over time in conjunction with major geologic events. Phylogenetic comparative analysis reveal an overriding signal of decreasing rates of trait evolution through time. Furthermore, the data suggest two major rate shifts in trait evolution associated with bursts of evolutionary innovation. The first rate shift occurs in the aftermath of the Great Oxidation Event and “Snowball Earth” glaciations and is associated with decrease in the evolutionary rates around 1.8–1.6 Ga. This rate shift seems to indicate the end of a major diversification of cyanobacterial phenotypes–particularly related to traits associated with filamentous morphology, heterocysts and motility in freshwater ecosystems. Another burst appears around the time of the Neoproterozoic Oxidation Event in the Neoproterozoic, and is associated with the acquisition of traits involved in planktonic growth in marine habitats. Our results demonstrate how uniting genomic and phenotypic datasets in extant bacterial species can shed light on billion-year old events in Earth’s history.

The role of microaerophilic Fe-oxidizing micro-organisms in producing banded iron formations

Despite the historical and economic significance of banded iron formations (BIFs), we have yet to resolve the formation mechanisms. On modern Earth, neutrophilic microaerophilic Fe-oxidizing micro-organisms (FeOM) produce copious amounts of Fe oxyhydroxides, leading us to wonder whether similar organisms played a role in producing BIFs. To evaluate this, we review the current knowledge of modern microaerophilic FeOM in the context of BIF paleoenvironmental studies. In modern environments wherever Fe(II) and O2 co-exist, microaerophilic FeOM proliferate. These organisms grow in a variety of environments, including the marine water column redoxcline, which is where BIF precursor minerals likely formed. FeOM can grow across a range of O2 concentrations, measured as low as 2 μm to date, although lower concentrations have not been tested. While some extant FeOM can tolerate high O2 concentrations, many FeOM appear to prefer and thrive at low O2 concentrations (~3-25 μm). These are similar to the estimated dissolved O2 concentrations in the few hundred million years prior to the 'Great Oxidation Event' (GOE). We compare biotic and abiotic Fe oxidation kinetics in the presence of varying levels of O2 and show that microaerophilic FeOM contribute substantially to Fe oxidation, at rates fast enough to account for BIF deposition. Based on this synthesis, we propose that microaerophilic FeOM were capable of playing a significant role in depositing the largest, most well-known BIFs associated with the GOE, as well as afterward when global O2 levels increased.

Oxidative elemental cycling under the low O2 Eoarchean atmosphere

The Great Oxidation Event signals the first large-scale oxygenation of the atmosphere roughly 2.4 Gyr ago. Geochemical signals diagnostic of oxidative weathering, however, extend as far back as 3.3-2.9 Gyr ago. 3.8-3.7 Gyr old rocks from Isua, Greenland stand as a deep time outpost, recording information on Earth's earliest surface chemistry and the low oxygen primordial biosphere. Here we find fractionated Cr isotopes, relative to the igneous silicate Earth reservoir, in metamorphosed banded iron formations (BIFs) from Isua that indicate oxidative Cr cycling 3.8-3.7 Gyr ago. Elevated U/Th ratios in these BIFs relative to the contemporary crust, also signal oxidative mobilization of U. We suggest that reactive oxygen species were present in the Eoarchean surface environment, under a very low oxygen atmosphere, inducing oxidative elemental cycling during the deposition of the Isua BIFs and possibly supporting early aerobic biology.

Open Questions on the Origin of Eukaryotes

Despite recent progress, the origin of the eukaryotic cell remains enigmatic. It is now known that the last eukaryotic common ancestor was complex and that endosymbiosis played a crucial role in eukaryogenesis at least via the acquisition of the alphaproteobacterial ancestor of mitochondria. However, the nature of the mitochondrial host is controversial, although the recent discovery of an archaeal lineage phylogenetically close to eukaryotes reinforces models proposing archaea-derived hosts. We argue that, in addition to improved phylogenomic analyses with more comprehensive taxon sampling to pinpoint the closest prokaryotic relatives of eukaryotes, determining plausible mechanisms and selective forces at the origin of key eukaryotic features, such as the nucleus or the bacterial-like eukaryotic membrane system, is essential to constrain existing models.

A fresh look at the evolution and diversification of photochemical reaction centers

In this review, I reexamine the origin and diversification of photochemical reaction centers based on the known phylogenetic relations of the core subunits, and with the aid of sequence and structural alignments. I show, for example, that the protein folds at the C-terminus of the D1 and D2 subunits of Photosystem II, which are essential for the coordination of the water-oxidizing complex, were already in place in the most ancestral Type II reaction center subunit. I then evaluate the evolution of reaction centers in the context of the rise and expansion of the different groups of bacteria based on recent large-scale phylogenetic analyses. I find that the Heliobacteriaceae family of Firmicutes appears to be the earliest branching of the known groups of phototrophic bacteria; however, the origin of photochemical reaction centers and chlorophyll synthesis cannot be placed in this group. Moreover, it becomes evident that the Acidobacteria and the Proteobacteria shared a more recent common phototrophic ancestor, and this is also likely for the Chloroflexi and the Cyanobacteria. Finally, I argue that the discrepancies among the phylogenies of the reaction center proteins, chlorophyll synthesis enzymes, and the species tree of bacteria are best explained if both types of photochemical reaction centers evolved before the diversification of the known phyla of phototrophic bacteria. The primordial phototrophic ancestor must have had both Type I and Type II reaction centers.

Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites

Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes) or other metabolisms (e.g., anoxygenic photosynthesis, sulfate reduction), may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico) by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W) and Northern (AL-N) shores of the lake and, at the latter site, along a depth gradient (1, 5, 10, and 15 m depth). The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria), Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM) observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at macroscale, and suggest a potential causal link. Despite the previous identification of intracellularly calcifying cyanobacteria in Alchichica microbialites, most carbonate precipitation seems extracellular in this system.

In situ trace metal analysis of Neoarchaean--Ordovician shallow-marine microbial-carbonate-hosted pyrites

Pre-Cambrian atmospheric and oceanic redox evolutions are expressed in the inventory of redox-sensitive trace metals in marine sedimentary rocks. Most of the currently available information was derived from deep-water sedimentary rocks (black shale/banded iron formation). Many of the studied trace metals (e.g. Mo, U, Ni and Co) are sensitive to the composition of the exposed land surface and prevailing weathering style, and their oceanic inventory ultimately depends on the terrestrial flux. The validity of claims for increased/decreased terrestrial fluxes has remained untested as far as the shallow-marine environment is concerned. Here, the first systematic study of trace metal inventories of the shallow-marine environment by analysis of microbial carbonate-hosted pyrite, from ca. 2.65-0.52 Ga, is presented. A petrographic survey revealed a first-order difference in preservation of early diagenetic pyrite. Microbial carbonates formed before the 2.4 Ga great oxygenation event (GOE) are much richer in pyrite and contain pyrite grains of greater morphological variability but lesser chemical substitution than samples deposited after the GOE. This disparity in pyrite abundance and morphology is mirrored by the qualitative degree of preservation of organic matter (largely as kerogen). Thus, it seems that in microbial carbonates, pyrite formation and preservation were related to presence and preservation of organic C. Several redox-sensitive trace metals show interpretable temporal trends supporting earlier proposals derived from deep-water sedimentary rocks. Most notably, the shallow-water pyrite confirms a rise in the oceanic Mo inventory across the pre-Cambrian-Cambrian boundary, implying the establishment of efficient deep-ocean ventilation. The carbonate-hosted pyrite also confirms the Neoarchaean and early Palaeoproterozoic ocean had higher Ni concentration, which can now more firmly be attributed to a greater proportion of magnesian volcanic rock on land rather than a stronger hydrothermal flux of Ni. Additionally, systematic trends are reported for Co, As, and Zn, relating to terrestrial flux and oceanic productivity.

Paleobiological Perspectives on Early Microbial Evolution

Microfossils, stromatolites, and chemical biosignatures indicate that Earth became a biological planet more than 3.5 billion years ago, making most of life's history microbial. Proterozoic rocks preserve a rich record of cyanobacteria, including derived forms that differentiate multiple cell types. Stromatolites, in turn, show that microbial communities covered the seafloor from tidal flats to the base of the photic zone. The Archean record is more challenging to interpret, particularly on the question of cyanobacterial antiquity, which remains to be resolved. In the late Neoproterozoic Era, increasing oxygen and radiating eukaryotes altered the biosphere, with planktonic algae gaining ecological prominence in the water column, whereas seaweeds and, eventually, animals spread across shallow seafloors. From a microbial perspective, however, animals, algae, and, later, plants simply provided new opportunities for diversification, and, to this day, microbial metabolisms remain the only essential components of biogeochemical cycles.