Electrons, life and the evolution of Earth's oxygen cycle

Is our understanding of aquatic ecosystems sufficient to quantify ecologically driven climate feedbacks?

The Earth functions as an integrated system-its current habitability to complex life is an emergent property dependent on interactions among biological, chemical, and physical components. As global warming affects ecosystem structure and function, so too will the biosphere affect climate by altering atmospheric gas composition and planetary albedo. Constraining these ecosystem-climate feedbacks is essential to accurately predict future change and develop mitigation strategies; however, the interplay among ecosystem processes complicates the assessment of their impact. Here, we explore the state-of-knowledge on how ecological and biological processes (e.g., competition, trophic interactions, metabolism, and adaptation) affect the directionality and magnitude of feedbacks between ecosystems and climate, using illustrative examples from the aquatic sphere. We argue that, despite ample evidence for the likely significance of many, our present understanding of the combinatorial effects of ecosystem dynamics precludes the robust quantification of most ecologically driven climate feedbacks. Constraining these effects must be prioritized within the ecological sciences for only by studying the biosphere as both subject and arbiter of global climate can we develop a sufficiently holistic view of the Earth system to accurately predict Earth's future and unravel its past.

Chapter 5: Major Biological Innovations in the History of Life on Earth

All organisms living on Earth descended from a single, common ancestral population of cells, known as LUCA-the last universal common ancestor. Since its emergence, the diversity and complexity of life have increased dramatically. This chapter focuses on four key biological innovations throughout Earth's history that had a significant impact on the expansion of phylogenetic diversity, organismal complexity, and ecospace habitation. First is the emergence of the last universal common ancestor, LUCA, which laid the foundation for all life-forms on Earth. Second is the evolution of oxygenic photosynthesis, which resulted in global geochemical and biological transformations. Third is the appearance of a new type of cell-the eukaryotic cell-which led to the origin of a new domain of life and the basis for complex multicellularity. Fourth is the multiple independent origins of multicellularity, resulting in the emergence of a new level of complex individuality. A discussion of these four key events will improve our understanding of the intertwined history of our planet and its inhabitants and better inform the extent to which we can expect life at different degrees of diversity and complexity elsewhere.

Enhanced nitrogen removal in low-carbon saline wastewater by adding functional bacteria into Sesuvium portulacastrum constructed wetlands

Functional bacterial communities (FBC) have members of different taxonomic biochemical groups, such as N2-fixation, nitrification and denitrification. This study explored the mechanism of the FBC from an upflow three-dimensional biofilm electrode reactor on enhancing the nitrogen removal efficiencies in a Sesuvium potulacastum (S. potulacastum) constructed wetland. There were high abundances of denitrifying bacteria detected in the FBC, and they had potential metabolic processes for nitrogen reduction. In the constructed wetland, cellular nitrogen compounds of S. potulacastum were enriched by overexpressed differentially expressed genes (DEGs), and the napA, narG, nirK, nirS, qnorB, and NosZ genes related to the denitrification process had more copies under FBC treatment. Nitrogen metabolism in root bacterial communities (RBCs) was activated in the FBC group compared with the control group without FBC. Finally, these FBCs improved the removal efficiencies of DTN (dissolved total nitrogen), NO3¯-N, NO2¯-N, and NH4+-N by 84.37 %, 87.42 %, 67.51 %, and 92.57 %, respectively, and their final concentrations met the emission standards of China. These findings indicate that adding FBC into S. potulacastum-constructed wetlands would result in high nitrogen removal efficiencies from wastewater and have large potential applications in further water treatment technology.

Bioactive Compounds of the Mediterranean Diet as Nutritional Support to Fight Neurodegenerative Disease

Neurodegenerative disorders are a widespread cause of morbidity and mortality worldwide, characterized by neuroinflammation, oxidative stress, and neuronal depletion. They include selective malfunction and progressive loss of neurons, glial cells, and neural networks in the brain and spinal cord. There is an urgent need to develop new and more effective therapeutic strategies to combat these devastating diseases because, today, there is no treatment that can cure degenerative diseases; however, we have many symptomatic treatments. Current nutritional approaches are beginning to reflect a fundamental change in our understanding of health. The Mediterranean diet may have a protective effect on the neurodegenerative process because it is rich in antioxidants, fiber, and omega-3 polyunsaturated fatty acids. Increasing knowledge regarding the impact of diet on regulation at the genetic and molecular levels is changing the way we consider the role of nutrition, resulting in new dietary strategies. Natural products, thanks to their bioactive compounds, have recently undergone extensive exploration and study for their therapeutic potential for a variety of diseases. Targeting simultaneous multiple mechanisms of action and a neuroprotection approach with the diet could prevent cell death and restore function to damaged neurons. For these reasons, this review will be focused on the therapeutic potential of natural products and the associations between the Mediterranean-style diet (MD), neurodegenerative diseases, and markers and mechanisms of neurodegeneration.

Structure of Photosystem I Supercomplex Isolated from a Chlamydomonas reinhardtii Cytochrome b6f Temperature-Sensitive Mutant

The unicellular green alga, Chlamydomonas reinhardtii, has been widely used as a model system to study photosynthesis. Its possibility to generate and analyze specific mutants has made it an excellent tool for mechanistic and biogenesis studies. Using negative selection of ultraviolet (UV) irradiation–mutated cells, we isolated a mutant (TSP9) with a single amino acid mutation in the Rieske protein of the cytochrome b6f complex. The W143R mutation in the petC gene resulted in total loss of cytochrome b6f complex function at the non-permissive temperature of 37 °C and recovery at the permissive temperature of 25 °C. We then isolated photosystem I (PSI) and photosystem II (PSII) supercomplexes from cells grown at the non-permissive temperature and determined the PSI structure with high-resolution cryogenic electron microscopy. There were several structural alterations compared with the structures obtained from wild-type cells. Our structural data suggest that the mutant responded by excluding the Lhca2, Lhca9, PsaL, and PsaH subunits. This structural alteration prevents state two transition, where LHCII migrates from PSII to bind to the PSI complex. We propose this as a possible response mechanism triggered by the TSP9 phenotype at the non-permissive temperature.

Rubisco, the imperfect winner: it's all about the base

Rubisco catalysis is complex and includes an activation step through the formation of a carbamate at the conserved active site lysine residue and the formation of a highly reactive enediol that is the key to its catalytic reaction. The formation of this enediol is both the basis of its success and its Achilles' heel, creating imperfections to its catalytic efficiency. While Rubisco originally evolved in an atmosphere of high CO2, the earth's multiple oxidation events provided challenges to Rubisco through the fixation of O2 that competes with CO2 at the active site. Numerous catalytic screens across the Rubisco superfamily have identified significant variation in catalytic properties that have been linked to large and small subunit sequences. Despite this, we still have a rudimentary understanding of Rubisco's catalytic mechanism and how the evolution of kinetic properties has occurred. This review identifies the lysine base that functions both as an activator and a proton abstractor to create the enediol as a key to understanding how Rubisco may optimize its kinetic properties. The ways in which Rubisco and its partners have overcome catalytic and activation imperfections and thrived in a world of high O2, low CO2, and variable climatic regimes is remarkable.

Dynamic changes of gut bacterial communities present in larvae of Anoplophora glabripennies collected at different developmental stages

The Asian long-horned beetle, Anoplophora glabripennies (Motschulsky), is a destructive wood-boring pest that is capable of killing healthy trees. Gut bacteria in the larvae of the wood-boring pest is essential for the fitness of hosts. However, little is known about the structure of the intestinal microbiome of A. glabripennies during larval development. Here, we used Illumina MiSeq high-throughput sequencing technology to analyze the larval intestinal bacterial communities of A. glabripennies at the stages of newly hatched larvae, 1st instar larvae and 4th instar larvae. Significant differences were found in larval gut microbial community structure at different larvae developmental stages. Different dominant genus was detected during larval development. Acinetobacter were dominant in the newly hatched larvae, Enterobacter and Raoultella in the 1st instar larvae, and Enterococcus and Gibbsiella in the 4th instar larvae. The microbial richness in the newly hatched larvae was higher than those in the 1st and 4th instar larvae. Many important functions of the intestinal microbiome were predicted, for example, fermentation and chemoheterotrophy functions that may play an important role in insect growth and development was detected in the bacteria at all tested stages. However, some specific functions are found to be associated with different development stages. Our study provides a theoretical basis for investigating the function of the intestinal symbiosis bacteria of A. glabripennies.

Magnetic fields and apoptosis: a possible mechanism

The potential therapeutic uses of electromagnetic fields (EMF), part of the nonionizing radiation spectrum, increase with time. Among them, those considering the potential antitumor effects exerted by the Magnetic Fields (MFs), part of the EMF entity, have gained more and more interest. A recent review on this subject reports the MFs' effect on apoptosis of tumor cells as one of the most important breakthroughs. Apoptosis is considered a key mechanism regulating the genetic stability of cells and as such is considered of fundamental importance in cancer initiation and development. According to an atomic/sub-atomic analysis, based on quantum physics, of the complexity of biological life and the role played by oxygen and its radicals in cancer biology, a possible biophysical mechanism is described. The mechanism considers the influence of MFs on apoptosis through an effect on electron spin that is able to increase reactive oxygen species (ROS) concentration. Impacting on the delicate balance between ROS production and ROS elimination in tumor cells is considered a promising cancer therapy, affecting different biological processes, such as apoptosis and metastasis. An analysis in the literature, which allows correlation between MFs exposure characteristics and their influence on apoptosis and ROS concentration, supports the validity of the mechanism.

Circadian clocks' interactions with oxygen sensing and signalling

In mammals, physiology and metabolism are shaped both by immediate and anticipatory responses to environmental changes through the myriad of molecular mechanisms. Whilst the former is mostly mediated through different acute signalling pathways the latter is primarily orchestrated by the circadian clock. Oxygen is vital for life and as such mammals have evolved different mechanisms to cope with changes in oxygen levels. It is widely accepted that oxygen sensing through the HIF-1 signalling pathway is paramount for the acute response to changes in oxygen levels. Circadian clocks are molecular oscillators that control 24 hours rhythms in various aspects of physiology and behaviour. Evidence emerging in recent years points towards pervasive molecular and functional interactions between these two pathways on multiple levels. Daily oscillations in oxygen levels are circadian clock-controlled and can reset the clock through HIF-1. Furthermore, the circadian clock appears to modulate the hypoxic response. We review herein the literature related to the crosstalk between the circadian clockwork and the oxygen-signalling pathway in mammals at the molecular and physiological level both under normal and pathologic conditions.

Hydrogen Peroxide in Ecological and Environmental Chemistry

This review paper is focused on the detailed consideration of the structure, properties and reactions of H2O2. The paper highlights the importance of revealing these processes’ mechanisms, since they have been insufficiently studied so far, or the related data have a fragmentary and incomplete character. A special attention is given to catalytic oxidation reactions, formation and properties of intermediates, their role in the natural environment.

Radiation of nitrogen-metabolizing enzymes across the tree of life tracks environmental transitions in Earth history

Nitrogen is an essential element to life and exerts a strong control on global biological productivity. The rise and spread of nitrogen-utilizing microbial metabolisms profoundly shaped the biosphere on the early Earth. Here, we reconciled gene and species trees to identify birth and horizontal gene transfer events for key nitrogen-cycling genes, dated with a time-calibrated tree of life, in order to examine the timing of the proliferation of these metabolisms across the tree of life. Our results provide new insights into the evolution of the early nitrogen cycle that expand on geochemical reconstructions. We observed widespread horizontal gene transfer of molybdenum-based nitrogenase back to the Archean, minor horizontal transfer of genes for nitrate reduction in the Archean, and an increase in the proliferation of genes metabolizing nitrite around the time of the Mesoproterozoic (~1.5 Ga). The latter coincides with recent geochemical evidence for a mid-Proterozoic rise in oxygen levels. Geochemical evidence of biological nitrate utilization in the Archean and early Proterozoic may reflect at least some contribution of dissimilatory nitrate reduction to ammonium (DNRA) rather than pure denitrification to N₂ . Our results thus help unravel the relative dominance of two metabolic pathways that are not distinguishable with current geochemical tools. Overall, our findings thus provide novel constraints for understanding the evolution of the nitrogen cycle over time and provide insights into the bioavailability of various nitrogen sources in the early Earth with possible implications for the emergence of eukaryotic life.

Nose-to-Brain Delivery of Antioxidants as a Potential Tool for the Therapy of Neurological Diseases

Oxidative stress has a key role in the pathogenesis of neurodegenerative disorders such as Alzheimer's, Parkinson's, and Huntington's diseases and can be an important cause of the damages in cerebral ischemia. Oxidative stress arises from high levels of reactive oxygen species (ROS). Consequently, on this rational base, antioxidants (many of natural origin) are proposed as potential drugs to prevent ROS noxious actions because they can protect the target tissues from the oxidative stress. However, the potential of antioxidants is limited, owing to the presence of the blood-brain barrier (BBB), which is difficult to cross with a consequent low bioavailability of the drug into the brain after systemic (intravenous, intraperitoneal, oral) administrations. One strategy to improve the delivery of antioxidants to the brain involves the use of the so-called nose-to-brain route, with the administration of the antioxidant in specific nasal formulations and its passage to the central nervous system (CNS) mainly through the olfactory nerve way. In the current literature, many examples show encouraging results in studies carried out in cell cultures and in animal models about the potential neuroprotective effects of antioxidants when administered through the nose. This review concerns the nose-to-brain route for the brain targeting of antioxidants as a potential tool for the therapy of neurological diseases.

Neuroprotective effects of natural compounds on neurotoxin-induced oxidative stress and cell apoptosis

OBJECTIVES

Overproduction of reactive species, notably reactive oxygen (ROS) and nitrogen (RNS) species, along with the failure of balancing effects of endogenous antioxidant defenses result in destruction of cellular structures, lipids, proteins, and genetic material, which lead to oxidative stress. Oxidative stress-induced neuronal apoptosis plays a pivotal role in pathogenesis of neurodegeneration. Antioxidants represent one of the medical choice strategies for protecting against this unbalanced oxidation-antioxidation status. Recently, natural compounds with neuroprotective potential that can scavenge free radicals and protect cells from oxidative damage have received extensive attention.

METHODS

In this review, we summarized the detailed research progress on the medicinal plants-derived natural compounds with potential anti-oxidation effects and their molecular mechanisms on modulating the neurotoxin (6-OHDA, H₂O₂, glutamate, Aβ)-induced oxidative stress and cell apoptosis.

RESULTS

The natural compounds that efficacious in modulating reactive species production and mitochondrial function include flavonoids, glucosides, alkaloids, polyphenols, lignans, coumarins, terpenoids, quinones and others. They decreased the neurotoxin-induced oxidative damage and apoptosis by (1) decreasing ROS/RNS generation, lipid peroxidation, caspase-3 and caspase-9 activities, LDH release, the ratio of Bax/Bcl-2, Ca²⁺ influx and cytochrome c release, (2) elevating MMP, and (3) restoring endogenous antioxidant enzymatic activities (CAT, GSH-Px, GSR, SOD). And they exerted neuroprotective effects against cell damages and apoptosis by modulating the oxidative cascades of different signaling pathways (Nrf2/HO-1, NF-κB, MAPKs, PI3K/Akt, GSK-3β) and preventing mitochondria-dependent apoptosis pathways.

DISCUSSION

The present work reviews the role of oxidative stress in neurodegeneration, highlighting the potential anti-oxidation effects of natural compounds as a promising approach to develop innovative neuroprotective strategy.

Microbial Nitrogen Cycling in Antarctic Soils

The Antarctic continent is widely considered to be one of the most hostile biological habitats on Earth. Despite extreme environmental conditions, the ice-free areas of the continent, which constitute some 0.44% of the total continental land area, harbour substantial and diverse communities of macro-organisms and especially microorganisms, particularly in the more "hospitable" maritime regions. In the more extreme non-maritime regions, exemplified by the McMurdo Dry Valleys of South Victoria Land, nutrient cycling and ecosystem servicing processes in soils are largely driven by microbial communities. Nitrogen turnover is a cornerstone of ecosystem servicing. In Antarctic continental soils, specifically those lacking macrophytes, cold-active free-living diazotrophic microorganisms, particularly Cyanobacteria, are keystone taxa. The diazotrophs are complemented by heterotrophic bacterial and archaeal taxa which show the genetic capacity to perform elements of the entire N cycle, including nitrification processes such as the anammox reaction. Here, we review the current literature on nitrogen cycling genes, taxa, processes and rates from studies of Antarctic soils. In particular, we highlight the current gaps in our knowledge of the scale and contribution of these processes in south polar soils as critical data to underpin viable predictions of how such processes may alter under the impacts of future climate change.

Anoxic photogeochemical oxidation of manganese carbonate yields manganese oxide

The oxidation states of manganese minerals in the geological record have been interpreted as proxies for the evolution of molecular oxygen in the Archean eon. Here we report that an Archean manganese mineral, rhodochrosite (MnCO3), can be photochemically oxidized by light under anoxic, abiotic conditions. Rhodochrosite has a calculated bandgap of about 5.4 eV, corresponding to light energy centering around 230 nm. Light at that wavelength would have been present on Earth's surface in the Archean, prior to the formation of stratospheric ozone. We show experimentally that the photooxidation of rhodochrosite in suspension with light centered at 230 nm produced H2 gas and manganite (γ-MnOOH) with an apparent quantum yield of 1.37 × 10-3 moles hydrogen per moles incident photons. Our results suggest that manganese oxides could have formed abiotically on the surface in shallow waters and on continents during the Archean eon in the absence of molecular oxygen.

Antioxidant Alternatives in the Treatment of Amyotrophic Lateral Sclerosis: A Comprehensive Review

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that produces a selective loss of the motor neurons of the spinal cord, brain stem and motor cortex. Oxidative stress (OS) associated with mitochondrial dysfunction and the deterioration of the electron transport chain has been shown to be a factor that contributes to neurodegeneration and plays a potential role in the pathogenesis of ALS. The regions of the central nervous system affected have high levels of reactive oxygen species (ROS) and reduced antioxidant defenses. Scientific studies propose treatment with antioxidants to combat the characteristic OS and the regeneration of nicotinamide adenine dinucleotide (NAD+) levels by the use of precursors. This review examines the possible roles of nicotinamide riboside and pterostilbene as therapeutic strategies in ALS.

An enzymatic method for precise oxygen affinity measurements over nanomolar-to-millimolar concentration regime

Oxygen affinity is an important property of metalloproteins that helps elucidate their reactivity profile and mechanism. Heretofore, oxygen affinity values were determined either using flash photolysis and polarography techniques that require expensive instrumentation, or using oxygen titration methods which are erroneous at low nanomolar and at high millimolar oxygen concentrations. Here, we describe an inexpensive, easy-to-setup, and a one-pot method for oxygen affinity measurements that uses the enzyme chlorite dismutase (Cld) as a precise in situ oxygen source. Using this method, we measure thermodynamic and kinetic oxygen affinities (K_d and K_M) of different classes of heme and non-heme metalloproteins involved in oxygen transport, sensing, and catalysis. The method enables oxygen affinity measurements over a wide concentration range from 10 nM to 5 mM which is unattainable by simply diluting oxygen-saturated buffers. In turn, we were able to precisely measure oxygen affinities of a model set of eight different metalloproteins with affinities ranging from 48 ± 3 nM to 1.18 ± 0.03 mM. Overall, the Cld method is easy and inexpensive to set up, requires significantly lower quantities of protein, enables precise oxygen affinity measurements, and is applicable for proteins exhibiting nanomolar-to-millimolar affinity values.

Does the Evolution of Complex Life Depend on the Stellar Spectral Energy Distribution?

This article presents the proportional evolutionary time (PET) hypothesis, which posits that the mean time required for the evolution of complex life is a function of stellar mass. The "biological available window" is defined as the region of a stellar spectrum between 200 and 1200 nm that generates free energy for life. Over the ∼4 Gyr history of Earth, the total energy incident at the top of the atmosphere and within the biological available window is ∼10³⁴ J. The hypothesis assumes that the rate of evolution from the origin of life to complex life is proportional to this total energy, which would suggest that planets orbiting other stars should not show signs of complex life if the total energy incident on the planet is below this energy threshold. The PET hypothesis predicts that late K- and M-dwarf stars (M < 0.7 [Formula: see text]) are too young to host any complex life at the present age of the Universe. F-, G-, and early K-dwarf stars (M > 0.7 [Formula: see text]) represent the best targets for the next generation of space telescopes to search for spectroscopic biosignatures indicative of complex life.

How to resurrect ancestral proteins as proxies for ancient biogeochemistry

Throughout the history of life, enzymes have served as the primary molecular mediators of biogeochemical cycles by catalyzing the metabolic pathways that interact with geochemical substrates. The byproducts of enzymatic activities have been preserved as chemical and isotopic signatures in the geologic record. However, interpretations of these signatures are limited by the assumption that such enzymes have remained functionally conserved over billions of years of molecular evolution. By reconstructing ancient genetic sequences in conjunction with laboratory enzyme resurrection, preserved biogeochemical signatures can instead be related to experimentally constrained, ancestral enzymatic properties. We may thereby investigate instances within molecular evolutionary trajectories potentially tied to significant biogeochemical transitions evidenced in the geologic record. Here, we survey recent enzyme resurrection studies to provide a reasoned assessment of areas of success and common pitfalls relevant to ancient biogeochemical applications. We conclude by considering the Great Oxidation Event, which provides a constructive example of a significant biogeochemical transition that warrants investigation with ancestral enzyme resurrection. This event also serves to highlight the pitfalls of facile interpretation of paleophenotype models and data, as applied to two examples of enzymes that likely both influenced and were influenced by the rise of atmospheric oxygen - RuBisCO and nitrogenase.

Tracing the Pathways of Waters and Protons in Photosystem II and Cytochrome c Oxidase

Photosystem II (PSII) uses water as the terminal electron donor, producing oxygen in the Mn4CaO5 oxygen evolving complex (OEC), while cytochrome c oxidase (CcO) reduces O2 to water in its heme–Cu binuclear center (BNC). Each protein is oriented in the membrane to add to the proton gradient. The OEC, which releases protons, is located near the P-side (positive, at low-pH) of the membrane. In contrast, the BNC is in the middle of CcO, so the protons needed for O2 reduction must be transferred from the N-side (negative, at high pH). In addition, CcO pumps protons from N- to P-side, coupled to the O2 reduction chemistry, to store additional energy. Thus, proton transfers are directly coupled to the OEC and BNC redox chemistry, as well as needed for CcO proton pumping. The simulations that study the changes in proton affinity of the redox active sites and the surrounding protein at different states of the reaction cycle, as well as the changes in hydration that modulate proton transfer paths, are described.

Role of APS reductase in biogeochemical sulfur isotope fractionation

Sulfur isotope fractionation resulting from microbial sulfate reduction (MSR) provides some of the earliest evidence of life, and secular variations in fractionation values reflect changes in biogeochemical cycles. Here we determine the sulfur isotope effect of the enzyme adenosine phosphosulfate reductase (Apr), which is present in all known organisms conducting MSR and catalyzes the first reductive step in the pathway and reinterpret the sedimentary sulfur isotope record over geological time. Small fractionations may be attributed to low sulfate concentrations and/or high respiration rates, whereas fractionations greater than that of Apr require a low chemical potential at that metabolic step. Since Archean sediments lack fractionation exceeding the Apr value of 20‰, they are indicative of sulfate reducers having had access to ample electron donors to drive their metabolisms. Large fractionations in post-Archean sediments are congruent with a decline of favorable electron donors as aerobic and other high potential metabolic competitors evolved.

Approaches to understanding the ecology and evolution of understudied terrestrial archaeal ammonia-oxidisers

Ammonia-oxidising archaea (AOA) form a phylogenetic group within the phylum Thaumarchaeota and are of ecological significance due to their role in nitrification, an important biogeochemical process. Previous research has provided information on their ecosystem role and potential physiological characteristics, for example, through analyses of their environmental distribution, ecological adaptation and evolutionary history. However, most AOA diversity, assessed using several environmental marker genes, is not represented in laboratory cultures, with consequent gaps in knowledge of their physiology and evolution. The present study critically reviews existing and developing approaches for the assessment of AOA function and diversity and their potential to provide a deeper understanding of these ecologically important, but understudied microorganisms.

Element strategy of oxygen evolution electrocatalysis based on in situ spectroelectrochemistry

Oxygen evolution electrocatalysis has received extensive attention due to its significance in biology, chemistry, and technology. However, it is still unclear how the abundant 3d-elements can be used to drive the four-electron oxidation of water as efficiently as in Nature. In this Feature Article, we will propose a design strategy concerning the optimization of the charge accumulation process based on our ongoing spectroelectrochemical study on Mn, Fe, and Ir oxygen evolution catalysts. Spectroscopic identification of the reaction intermediates showed that the activity of MnO₂ and Fe₂O₃ was dictated by the generation of Mn³⁺ and Fe⁴⁺, whereas in the case of IrO_x, the activity did not correlate with the valence change of Ir. The efficiency of charge accumulation through valence change is closely linked with the spin configuration of the metal center, because charge disproportionation, which was found to inhibit charge accumulation in the high-spin 3d metals, requires an electron in the e_g orbital. In addition to directly increasing the overpotential through the generation of an unstable intermediate, charge disproportionation inhibits charge accumulation by dissipating the total oxidative energy of the system. A favorable charge accumulation process may also be beneficial for electrode kinetics due to the enhanced coupling between reaction rates and electrochemical driving force. The model proposed in this study may help explain why low-spin 4d/5d rare metals are often more active than the abundant high-spin 3d materials for multi-electron transfer reactions in general, and provides new insight into how active 3d-metal catalysts can be synthesized by optimizing the energetics of both bond formation and charge accumulation.

Reflections on O2 as a Biosignature in Exoplanetary Atmospheres

Oxygenic photosynthesis is Earth's dominant metabolism, having evolved to harvest the largest expected energy source at the surface of most terrestrial habitable zone planets. Using CO₂ and H₂O-molecules that are expected to be abundant and widespread on habitable terrestrial planets-oxygenic photosynthesis is plausible as a significant planetary process with a global impact. Photosynthetic O₂ has long been considered particularly robust as a sign of life on a habitable exoplanet, due to the lack of known "false positives"-geological or photochemical processes that could also produce large quantities of stable O₂. O₂ has other advantages as a biosignature, including its high abundance and uniform distribution throughout the atmospheric column and its distinct, strong absorption in the visible and near-infrared. However, recent modeling work has shown that false positives for abundant oxygen or ozone could be produced by abiotic mechanisms, including photochemistry and atmospheric escape. Environmental factors for abiotic O₂ have been identified and will improve our ability to choose optimal targets and measurements to guard against false positives. Most of these false-positive mechanisms are dependent on properties of the host star and are often strongest for planets orbiting M dwarfs. In particular, selecting planets found within the conservative habitable zone and those orbiting host stars more massive than 0.4 M_⊙ (M3V and earlier) may help avoid planets with abundant abiotic O₂ generated by water loss. Searching for O₄ or CO in the planetary spectrum, or the lack of H₂O or CH₄, could help discriminate between abiotic and biological sources of O₂ or O₃. In advance of the next generation of telescopes, thorough evaluation of potential biosignatures-including likely environmental context and factors that could produce false positives-ultimately works to increase our confidence in life detection. Key Words: Biosignatures-Exoplanets-Oxygen-Photosynthesis-Planetary spectra. Astrobiology 17, 1022-1052.

Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment

Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.

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.

Dinitrogenase-Driven Photobiological Hydrogen Production Combats Oxidative Stress in Cyanothece sp. Strain ATCC 51142

Photobiologically synthesized hydrogen (H₂) gas is carbon neutral to produce and clean to combust, making it an ideal biofuel. Cyanothece sp. strain ATCC 51142 is a cyanobacterium capable of performing simultaneous oxygenic photosynthesis and H₂ production, a highly perplexing phenomenon because H₂ evolving enzymes are O₂ sensitive. We employed a system-level in vivo chemoproteomic profiling approach to explore the cellular dynamics of protein thiol redox and how thiol redox mediates the function of the dinitrogenase NifHDK, an enzyme complex capable of aerobic hydrogenase activity. We found that NifHDK responds to intracellular redox conditions and may act as an emergency electron valve to prevent harmful reactive oxygen species formation in concert with other cell strategies for maintaining redox homeostasis. These results provide new insight into cellular redox dynamics useful for advancing photolytic bioenergy technology and reveal a new understanding for the biological function of NifHDK.

IMPORTANCE

Here, we demonstrate that high levels of hydrogen synthesis can be induced as a protection mechanism against oxidative stress via the dinitrogenase enzyme complex in Cyanothece sp. strain ATCC 51142. This is a previously unknown feature of cyanobacterial dinitrogenase, and we anticipate that it may represent a strategy to exploit cyanobacteria for efficient and scalable hydrogen production. We utilized a chemoproteomic approach to capture the in situ dynamics of reductant partitioning within the cell, revealing proteins and reactive thiols that may be involved in redox sensing and signaling. Additionally, this method is widely applicable across biological systems to achieve a greater understanding of how cells navigate their environment and how redox chemistry can be utilized to alter metabolism and achieve homeostasis.

Oxidative Stress in Neurodegenerative Diseases

The pathophysiologies of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), Parkinson's disease (PD), and Alzheimer's disease (AD), are far from being fully explained. Oxidative stress (OS) has been proposed as one factor that plays a potential role in the pathogenesis of neurodegenerative disorders. Clinical and preclinical studies indicate that neurodegenerative diseases are characterized by higher levels of OS biomarkers and by lower levels of antioxidant defense biomarkers in the brain and peripheral tissues. In this article, we review the current knowledge regarding the involvement of OS in neurodegenerative diseases, based on clinical trials and animal studies. In addition, we analyze the effects of the drug-induced modulation of oxidative balance, and we explore pharmacotherapeutic strategies for OS reduction.

The Role of Microbial Electron Transfer in the Coevolution of the Biosphere and Geosphere

All life on Earth is dependent on biologically mediated electron transfer (i.e., redox) reactions that are far from thermodynamic equilibrium. Biological redox reactions originally evolved in prokaryotes and ultimately, over the first ∼2.5 billion years of Earth's history, formed a global electronic circuit. To maintain the circuit on a global scale requires that oxidants and reductants be transported; the two major planetary wires that connect global metabolism are geophysical fluids-the atmosphere and the oceans. Because all organisms exchange gases with the environment, the evolution of redox reactions has been a major force in modifying the chemistry at Earth's surface. Here we briefly review the discovery and consequences of redox reactions in microbes with a specific focus on the coevolution of life and geochemical phenomena.

Impact of metabolism and growth phase on the hydrogen isotopic composition of microbial fatty acids

Microorganisms are involved in all elemental cycles and therefore it is important to study their metabolism in the natural environment. A recent technique to investigate this is the hydrogen isotopic composition of microbial fatty acids, i.e., heterotrophic microorganisms produce fatty acids enriched in deuterium (D) while photoautotrophic and chemoautotrophic microorganisms produce fatty acids depleted in D compared to the water in the culture medium (growth water). However, the impact of factors other than metabolism have not been investigated. Here, we evaluate the impact of growth phase compared to metabolism on the hydrogen isotopic composition of fatty acids of different environmentally relevant microorganisms with heterotrophic, photoautotrophic and chemoautotrophic metabolisms. Fatty acids produced by heterotrophs are enriched in D compared to growth water with ε_lipid/water between 82 and 359‰ when grown on glucose or acetate, respectively. Photoautotrophs (ε_lipid/water between −149 and −264‰) and chemoautotrophs (ε_lipid/water between −217 and −275‰) produce fatty acids depleted in D. Fatty acids become, in general, enriched by between 4 and 46‰ with growth phase which is minor compared to the influence of metabolisms. Therefore, the D/H ratio of fatty acids is a promising tool to investigate community metabolisms in nature.

Evolutionary Aspects and Regulation of Tetrapyrrole Biosynthesis in Cyanobacteria under Aerobic and Anaerobic Environments

Chlorophyll a (Chl) is a light-absorbing tetrapyrrole pigment that is essential for photosynthesis. The molecule is produced from glutamate via a complex biosynthetic pathway comprised of at least 15 enzymatic steps. The first half of the Chl pathway is shared with heme biosynthesis, and the latter half, called the Mg-branch, is specific to Mg-containing Chl a. Bilin pigments, such as phycocyanobilin, are additionally produced from heme, so these light-harvesting pigments also share many common biosynthetic steps with Chl biosynthesis. Some of these common steps in the biosynthetic pathways of heme, Chl and bilins require molecular oxygen for catalysis, such as oxygen-dependent coproporphyrinogen III oxidase. Cyanobacteria thrive in diverse environments in terms of oxygen levels. To cope with Chl deficiency caused by low-oxygen conditions, cyanobacteria have developed elaborate mechanisms to maintain Chl production, even under microoxic environments. The use of enzymes specialized for low-oxygen conditions, such as oxygen-independent coproporphyrinogen III oxidase, constitutes part of a mechanism adapted to low-oxygen conditions. Another mechanism adaptive to hypoxic conditions is mediated by the transcriptional regulator ChlR that senses low oxygen and subsequently activates the transcription of genes encoding enzymes that work under low-oxygen tension. In diazotrophic cyanobacteria, this multilayered regulation also contributes in Chl biosynthesis by supporting energy production for nitrogen fixation that also requires low-oxygen conditions. We will also discuss the evolutionary implications of cyanobacterial tetrapyrrole biosynthesis and regulation, because low oxygen-type enzymes also appear to be evolutionarily older than oxygen-dependent enzymes.

Engineered Photosystem II reaction centers optimize photochemistry versus photoprotection at different solar intensities

The D1 protein of Photosystem II (PSII) provides most of the ligating amino acid residues for the Mn4CaO5 water-oxidizing complex (WOC) and half of the reaction center cofactors, and it is present as two isoforms in the cyanobacterium Synechococcus elongatus PCC 7942. These isoforms, D1:1 and D1:2, confer functional advantages for photosynthetic growth at low and high light intensities, respectively. D1:1, D1:2, and seven point mutations in the D1:2 background that are native to D1:1 were expressed in the green alga Chlamydomonas reinhardtii. We used these nine strains to show that those strains that confer a higher yield of PSII charge separation under light-limiting conditions (where charge recombination is significant) have less efficient photochemical turnover, measured in terms of both a lower WOC turnover probability and a longer WOC cycle period. Conversely, these same strains under light saturation (where charge recombination does not compete) confer a correspondingly faster O2 evolution rate and greater protection against photoinhibition. Taken together, the data clearly establish that PSII primary charge separation is a trade-off between photochemical productivity (water oxidation and plastoquinone reduction) and charge recombination (photoprotection). These trade-offs add up to a significant growth advantage for the two natural isoforms. These insights provide fundamental design principles for engineering of PSII reaction centers with optimal photochemical efficiencies for growth at low versus high light intensities.

Mapping the diatom redox-sensitive proteome provides insight into response to nitrogen stress in the marine environment

Diatoms are ubiquitous marine photosynthetic eukaryotes responsible for approximately 20% of global photosynthesis. Little is known about the redox-based mechanisms that mediate diatom sensing and acclimation to environmental stress. Here we used a quantitative mass spectrometry-based approach to elucidate the redox-sensitive signaling network (redoxome) mediating the response of diatoms to oxidative stress. We quantified the degree of oxidation of 3,845 cysteines in the Phaeodactylum tricornutum proteome and identified approximately 300 redox-sensitive proteins. Intriguingly, we found redox-sensitive thiols in numerous enzymes composing the nitrogen assimilation pathway and the recently discovered diatom urea cycle. In agreement with this finding, the flux from nitrate into glutamine and glutamate, measured by the incorporation of (15)N, was strongly inhibited under oxidative stress conditions. Furthermore, by targeting the redox-sensitive GFP sensor to various subcellular localizations, we mapped organelle-specific oxidation patterns in response to variations in nitrogen quota and quality. We propose that redox regulation of nitrogen metabolism allows rapid metabolic plasticity to ensure cellular homeostasis, and thus is essential for the ecological success of diatoms in the marine ecosystem.

Nitrate ammonification by Nautilia profundicola AmH: experimental evidence consistent with a free hydroxylamine intermediate

The process of nitrate reduction via nitrite controls the fate and bioavailability of mineral nitrogen within ecosystems; i.e., whether it is retained as ammonium (ammonification) or lost as nitrous oxide or dinitrogen (denitrification). Here, we present experimental evidence for a novel pathway of microbial nitrate reduction, the reverse hydroxylamine:ubiquinone reductase module (reverse-HURM) pathway. Instead of a classical ammonia-forming nitrite reductase that performs a 6 electron-transfer process, the pathway is thought to employ two catalytic redox modules operating in sequence: the reverse-HURM reducing nitrite to hydroxylamine followed by a hydroxylamine reductase that converts hydroxylamine to ammonium. Experiments were performed on Nautilia profundicola strain AmH, whose genome sequence led to the reverse-HURM pathway proposal. N. profundicola produced ammonium from nitrate, which was assimilated into biomass. Furthermore, genes encoding the catalysts of the reverse-HURM pathway were preferentially expressed during growth of N. profundicola on nitrate as an electron acceptor relative to cultures grown on polysulfide as an electron acceptor. Finally, nitrate-grown cells of N. profundicola were able to rapidly and stoichiometrically convert high concentrations of hydroxylamine to ammonium in resting cell assays. These experiments are consistent with the reverse-HURM pathway and a free hydroxylamine intermediate, but could not definitively exclude direct nitrite reduction to ammonium by the reverse-HURM with hydroxylamine as an off-pathway product. N. profundicola and related organisms are models for a new pathway of nitrate ammonification that may have global impact due to the wide distribution of these organisms in hypoxic environments and symbiotic or pathogenic associations with animal hosts.

Interactions of photosynthesis with genome size and function

Photolithotrophs are divided between those that use water as their electron donor (Cyanobacteria and the photosynthetic eukaryotes) and those that use a different electron donor (the anoxygenic photolithotrophs, all of them Bacteria). Photolithotrophs with the most reduced genomes have more genes than do the corresponding chemoorganotrophs, and the fastest-growing photolithotrophs have significantly lower specific growth rates than the fastest-growing chemoorganotrophs. Slower growth results from diversion of resources into the photosynthetic apparatus, which accounts for about half of the cell protein. There are inherent dangers in (especially oxygenic) photosynthesis, including the formation of reactive oxygen species (ROS) and blue light sensitivity of the water spitting apparatus. The extent to which photolithotrophs incur greater DNA damage and repair, and faster protein turnover with increased rRNA requirement, needs further investigation. A related source of environmental damage is ultraviolet B (UVB) radiation (280-320 nm), whose flux at the Earth's surface decreased as oxygen (and ozone) increased in the atmosphere. This oxygenation led to the requirements of defence against ROS, and decreasing availability to organisms of combined (non-dinitrogen) nitrogen and ferrous iron, and (indirectly) phosphorus, in the oxygenated biosphere. Differential codon usage in the genome and, especially, the proteome can lead to economies in the use of potentially growth-limiting elements.

Algal evolution in relation to atmospheric CO2: carboxylases, carbon-concentrating mechanisms and carbon oxidation cycles

Oxygenic photosynthesis evolved at least 2.4 Ga; all oxygenic organisms use the ribulose bisphosphate carboxylase-oxygenase (Rubisco)-photosynthetic carbon reduction cycle (PCRC) rather than one of the five other known pathways of autotrophic CO(2) assimilation. The high CO(2) and (initially) O(2)-free conditions permitted the use of a Rubisco with a high maximum specific reaction rate. As CO(2) decreased and O(2) increased, Rubisco oxygenase activity increased and 2-phosphoglycolate was produced, with the evolution of pathways recycling this inhibitory product to sugar phosphates. Changed atmospheric composition also selected for Rubiscos with higher CO(2) affinity and CO(2)/O(2) selectivity correlated with decreased CO(2)-saturated catalytic capacity and/or for CO(2)-concentrating mechanisms (CCMs). These changes increase the energy, nitrogen, phosphorus, iron, zinc and manganese cost of producing and operating Rubisco-PCRC, while biosphere oxygenation decreased the availability of nitrogen, phosphorus and iron. The majority of algae today have CCMs; the timing of their origins is unclear. If CCMs evolved in a low-CO(2) episode followed by one or more lengthy high-CO(2) episodes, CCM retention could involve a combination of environmental factors known to favour CCM retention in extant organisms that also occur in a warmer high-CO(2) ocean. More investigations, including studies of genetic adaptation, are needed.

Theory of the origin, evolution, and nature of life

Life is an inordinately complex unsolved puzzle. Despite significant theoretical progress, experimental anomalies, paradoxes, and enigmas have revealed paradigmatic limitations. Thus, the advancement of scientific understanding requires new models that resolve fundamental problems. Here, I present a theoretical framework that economically fits evidence accumulated from examinations of life. This theory is based upon a straightforward and non-mathematical core model and proposes unique yet empirically consistent explanations for major phenomena including, but not limited to, quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and amino acids, homeoviscous adaptation, triplet code, and DNA mutations. The theoretical framework unifies the macrocosmic and microcosmic realms, validates predicted laws of nature, and solves the puzzle of the origin and evolution of cellular life in the universe.

An evolutionary comparative scan for longevity-related oxidative stress resistance mechanisms in homeotherms

Key mechanisms relating oxidative stress to longevity from an interespecies comparative approach are reviewed. Long-lived animal species show low rates of reactive oxygen species (ROS) generation and oxidative damage at their mitochondria. Comparative physiology also shows that the specific compositional pattern of tissue macromolecules (proteins, lipids and nucleic acids) in long-lived animal species gives them an intrinsically high resistance to modification that likely contributes to their superior longevity. This is obtained in the case of lipids by decreasing the degree of fatty acid unsaturation, and in the case of proteins by lowering their methionine content. These findings are also substantiated from a phylogenomic approach. Nutritional or/and pharmacological interventions focused to modify some of these molecular traits were translated with modifications in animal longevity. It is proposed that natural selection tends to decrease the mitochondrial ROS generation and to increase the molecular resistance to the oxidative damage in long-lived species.

The cost of photoinhibition

Photoinhibition is an inevitable consequence of oxygenic photosynthesis. However, the concept of a 'photoinhibition-proof' plant in which photosystem II (PSII) is immune to photodamage is useful as a benchmark for considering the performances of plants with varying mixes of mechanisms which limit the extent of photodamage and which repair photodamage. Some photodamage is bound to occur, and the energy costs of repair are the direct costs of repair plus the photosynthesis foregone during repair. One mechanism permitting partial avoidance of photodamage is restriction of the number of photons incident on the photosynthetic apparatus per unit time, achieved by phototactic movement of motile algae to places with lower incident photosynthetically active radiation (PAR), by phototactic movement of plastids within cells to positions that minimize the incident PAR and by photonastic relative movements of parts of photolithotrophs attached to a substrate. The other means of avoiding photodamage is dissipating excitation of photosynthetic pigments including state transitions, non-photochemical quenching by one of the xanthophyll cycles or some other process and photochemical quenching by increased electron flow through PSII involving CO₂ and other acceptors, including the engagement of additional electron transport pathways. These mechanisms inevitably have the potential to decrease the rate of growth. As well as the decreased photosynthetic rates as a result of photodamage and the restrictions on photosynthesis imposed by the repair, avoidance, quenching and scavenging mechanisms, there are also additional energy, nitrogen and phosphorus costs of producing and operating repair, avoidance, quenching and scavenging mechanisms. A comparison is also made between the costs of photoinhibition and those of other plant functions impeded by the occurrence of oxygenic photosynthesis, i.e. the competitive inhibition of the carboxylase activity of ribulose bisphosphate carboxylase-oxygenase by oxygen via the oxygenase activity, and oxygen damage to nitrogenase in diazotrophic organisms.

Extreme 15N-enrichments in 2.72-Gyr-old sediments: evidence for a turning point in the nitrogen cycle

Although nitrogen is a key element in organic molecules such as nucleic acids and proteins, the timing of the emergence of its modern biogeochemical cycle is poorly known. Recent studies on the antiquity of the nitrogen cycle and its interaction with free oxygen suggests the establishment of a complete aerobic N biogeochemical cycle with nitrification, denitrification, and nitrogen fixation at about 2.68 Gyr. Here, we report new bulk nitrogen isotope data for the 2.72 billion-year-old sedimentary succession of the Tumbiana Formation (Pilbara Craton, Western Australia). The nitrogen isotopic compositions vary widely from +8.6‰ up to +50.4‰ and are inversely correlated with the very low δ(13)C values of associated organic matter defining the Fortescue excursion (down to about -56‰). We propose that this (15)N-enrichment records the onset of nitrification coupled to the continuous removal of its derivatives (nitrite and nitrate) by denitrification. This finding implies an increase in the availability of electron acceptors and probably oxygen in the Tumbiana depositional environment, 300 million years before the oxygenation of the Earth's atmosphere.

The evolution of new enzyme function: lessons from xenobiotic metabolizing bacteria versus insecticide-resistant insects

Here, we compare the evolutionary routes by which bacteria and insects have evolved enzymatic processes for the degradation of four classes of synthetic chemical insecticide. For insects, the selective advantage of such degradative activities is survival on exposure to the insecticide, whereas for the bacteria the advantage is simply a matter of access to additional sources of nutrients. Nevertheless, bacteria have evolved highly efficient enzymes from a wide variety of enzyme families, whereas insects have relied upon generalist esterase-, cytochrome P450- and glutathione-S-transferase-dependent detoxification systems. Moreover, the mutant insect enzymes are less efficient kinetically and less diverged in sequence from their putative ancestors than their bacterial counterparts. This presumably reflects several advantages that bacteria have over insects in the acquisition of new enzymatic functions, such as a broad biochemical repertoire from which new functions can be evolved, large population sizes, high effective mutation rates, very short generation times and access to genetic diversity through horizontal gene transfer. Both the insect and bacterial systems support recent theory proposing that new biochemical functions often evolve from 'promiscuous' activities in existing enzymes, with subsequent mutations then enhancing those activities. Study of the insect enzymes will help in resistance management, while the bacterial enzymes are potential bioremediants of insecticide residues in a range of contaminated environments.

Evolution of photosynthesis

Energy conversion of sunlight by photosynthetic organisms has changed Earth and life on it. Photosynthesis arose early in Earth's history, and the earliest forms of photosynthetic life were almost certainly anoxygenic (non-oxygen evolving). The invention of oxygenic photosynthesis and the subsequent rise of atmospheric oxygen approximately 2.4 billion years ago revolutionized the energetic and enzymatic fundamentals of life. The repercussions of this revolution are manifested in novel biosynthetic pathways of photosynthetic cofactors and the modification of electron carriers, pigments, and existing and alternative modes of photosynthetic carbon fixation. The evolutionary history of photosynthetic organisms is further complicated by lateral gene transfer that involved photosynthetic components as well as by endosymbiotic events. An expanding wealth of genetic information, together with biochemical, biophysical, and physiological data, reveals a mosaic of photosynthetic features. In combination, these data provide an increasingly robust framework to formulate and evaluate hypotheses concerning the origin and evolution of photosynthesis.

The geochemical record of the ancient nitrogen cycle, nitrogen isotopes, and metal cofactors

The nitrogen (N) cycle is the only global biogeochemical cycle that is driven by biological functions involving the interaction of many microorganisms. The N cycle has evolved over geological time and its interaction with the oxygen cycle has had profound effects on the evolution and timing of Earth's atmosphere oxygenation (Falkowski and Godfrey, 2008). Almost every enzyme that microorganisms use to manipulate N contains redox-sensitive metals. Bioavailability of these metals has changed through time as a function of varying redox conditions, and likely influenced the biological underpinnings of the N cycle. It is possible to construct a record through geological time using N isotopes and metal concentrations in sediments to determine when the different stages of the N cycle evolved and the role metal availability played in the development of key enzymes. The same techniques are applicable to understanding the operation and changes in the N cycle through geological time. However, N and many of the redox-sensitive metals in some of their oxidation states are mobile and the isotopic composition or distribution can be altered by subsequent processes leading to erroneous conclusions. This chapter reviews the enzymology and metal cofactors of the N cycle and describes proper utilization of methods used to reconstruct evolution of the N cycle through time.