Earth's Biosphere Research Articles

Chemostratigraphic and U–Pb geochronologic constraints on carbon cycling across the Silurian–Devonian boundary

The Devonian Period hosts extraordinary changes to Earth's biosphere. Land plants began their rise to prominence, with early vascular vegetation beginning its colonization of near-shore environments in the latest Silurian. Across the Silurian–Devonian (Pridoli–Lochkovian) transition, carbon isotope analyses of bulk marine carbonates (δCcarb13) from Laurentian and Baltic successions reveal a positive δCcarb13 shift. Known as the Klonk Event, values reach +5.8‰, making it one of the largest carbon isotope excursions in the Phanerozoic. Assigning rates and durations to these significant events requires a robust, precise Devonian time scale. Here we present 675 micritic matrix and 357 fossil-specific δCcarb13 analyses from the lower Devonian Helderberg Group of New York and West Virginia that exhibit the very positive δCcarb13 values observed in other Silurian–Devonian basins. This chemostratigraphic dataset is coupled with 66 ID-TIMS U–Pb dates on single zircons from six ash falls intercalated within Helderberg sediments, including dates on the stratigraphically lowest Devonian ashes yet developed. In this work, we (a) demonstrate that matrix and fossil-specific δCcarb13 values track one another closely in the Helderberg Group, (b) estimate the Silurian–Devonian boundary age in New York to be 421.3±1.2 Ma (2σ; including decay constant uncertainties), and (c) calculate the time required to evolve from baseline to peak δCcarb13 values at the onset of the Klonk event to be 1.00±0.25 Myr. Under these constraints, a steady-state perturbation to the global carbon cycle can explain the observed excursion with modern fluxes, as long as DIC concentration in the Devonian ocean remained below ∼2× the modern value. Therefore, potential drivers, such as enhanced burial of organic carbon, need not rely on anomalously high total fluxes of carbon to explain the Klonk Event.

Mitigating Geomagnetic Disturbances: A summary of Dominion Virginia Power?s efforts.

The Sun, the only star in our solar system, is an essential energy source for all human activities as well as the entire Earth biosphere. Galileo discovered the existence of sunspots in 1610, and 200 years later, Schwabe proved that our home star's activities follow a cycle of 11 years. Using high-tech devices, scientists and engineers have gained a clearer vision of solar activities and are now better able to discern the sun's behavior. Known solar activities include a combination of sunspots, solar flares, and coronal mass ejections. Solar activity occurs in peaks, with roughly equal intervals between them. The sun interacts significantly with Earth's magnetosphere. Extraordinary solar activities (or solar storms) can severely interfere with Earth's magnetospheric and ionospheric electrical current system, causing rapidly changing Earth surface potential (ESP). The destructive consequences become more evident with the ever-increasing propagation of electrical and electronic equipment. The first recorded example of the negative effects of solar activity on human society was an unprecedented solar storm that raged from 28 August through 2 September 1859 (cycle 10), in which telegraph systems all over Europe and North America failed.

Microbial ecology of Antarctic aquatic systems.

The Earth's biosphere is dominated by cold environments, and the cold biosphere is dominated by microorganisms. Microorganisms in cold Southern Ocean waters are recognized for having crucial roles in global biogeochemical cycles, including carbon sequestration, whereas microorganisms in other Antarctic aquatic biomes are not as well understood. In this Review, I consider what has been learned about Antarctic aquatic microbial ecology from 'omic' studies. I assess the factors that shape the biogeography of Antarctic microorganisms, reflect on some of the unusual biogeochemical cycles that they are associated with and discuss the important roles that viruses have in controlling ecosystem function.

Multiple oscillations in Neoarchaean atmospheric chemistry

The Great Oxidation Event (GOE) represents a crucial juncture in Earth history, signifying the rise in atmospheric oxygen from parts per million to percent levels at ∼2.45–2.32 billion-years-ago (Ga). Although planetary oxygenation undoubtedly led to the inception of the contemporary Earth system, the trigger(s) and mechanism(s) controlling this chemical reorganisation remain elusive. Quantitative estimates of the atmosphere's composition in the prelude to the GOE are central to understanding this oxygenation event. Previous analyses of 2.65–2.5 Ga sediments from the Griqualand Basin (South Africa) invoke a tantalising picture of an unusual Earth environment, alluding to an atmosphere periodically dominated by a layer of organic particles (“haze”) formed from methane photolysis. However, as yet this hypothesis has remained untested. Here we present four new coupled carbon and quadruple sulphur isotope records from distal, time equivalent (2.7–2.5 Ga), sedimentary successions from South Africa and Western Australia. These extended records reveal similar chemostratigraphic trends, supporting a dynamic terminal-Neoarchaean atmosphere, oscillating between a hazy state at elevated methane concentrations, and a haze-free anoxic background state. We suggest these atmospheric aberrations were related to heightened biogenic methane fluxes fuelled by enhanced nutrient delivery from climatically or weathering induced feedbacks. These data question the canonical view of a simple, unidirectional planetary oxygenation and signify that the overture to the GOE was governed by complex feedbacks within the Earth–biosphere system.

Evolvability Is an Evolved Ability: The Coding Concept as the Arch-Unit of Natural Selection.

Physical processes that characterize living matter are qualitatively distinct in that they involve encoding and transfer of specific types of information. Such information plays an active part in the control of events that are ultimately linked to the capacity of the system to persist and multiply. This algorithmicity of life is a key prerequisite for its Darwinian evolution, driven by natural selection acting upon stochastically arising variations of the encoded information. The concept of evolvability attempts to define the total capacity of a system to evolve new encoded traits under appropriate conditions, i.e., the accessible section of total morphological space. Since this is dependent on previously evolved regulatory networks that govern information flow in the system, evolvability itself may be regarded as an evolved ability. The way information is physically written, read and modified in living cells (the "coding concept") has not changed substantially during the whole history of the Earth's biosphere. This biosphere, be it alone or one of many, is, accordingly, itself a product of natural selection, since the overall evolvability conferred by its coding concept (nucleic acids as information carriers with the "rulebook of meanings" provided by codons, as well as all the subsystems that regulate various conditional information-reading modes) certainly played a key role in enabling this biosphere to survive up to the present, through alterations of planetary conditions, including at least five catastrophic events linked to major mass extinctions. We submit that, whatever the actual prebiotic physical and chemical processes may have been on our home planet, or may, in principle, occur at some time and place in the Universe, a particular coding concept, with its respective potential to give rise to a biosphere, or class of biospheres, of a certain evolvability, may itself be regarded as a unit (indeed the arch-unit) of natural selection.

Pelagic photoferrotrophy and iron cycling in a modern ferruginous basin.

Iron-rich (ferruginous) ocean chemistry prevailed throughout most of Earth’s early history. Before the evolution and proliferation of oxygenic photosynthesis, biological production in the ferruginous oceans was likely driven by photoferrotrophic bacteria that oxidize ferrous iron {Fe(II)} to harness energy from sunlight, and fix inorganic carbon into biomass. Photoferrotrophs may thus have fuelled Earth’s early biosphere providing energy to drive microbial growth and evolution over billions of years. Yet, photoferrotrophic activity has remained largely elusive on the modern Earth, leaving models for early biological production untested and imperative ecological context for the evolution of life missing. Here, we show that an active community of pelagic photoferrotrophs comprises up to 30% of the total microbial community in illuminated ferruginous waters of Kabuno Bay (KB), East Africa (DR Congo). These photoferrotrophs produce oxidized iron {Fe(III)} and biomass, and support a diverse pelagic microbial community including heterotrophic Fe(III)-reducers, sulfate reducers, fermenters and methanogens. At modest light levels, rates of photoferrotrophy in KB exceed those predicted for early Earth primary production, and are sufficient to generate Earth’s largest sedimentary iron ore deposits. Fe cycling, however, is efficient, and complex microbial community interactions likely regulate Fe(III) and organic matter export from the photic zone.

Searching for the best bet in life-strategy: A quantitative approach to individual performance and population dynamics in reef-building corals

Ecological signs of Earth's biosphere forewarn an alarming trajectory towards a global mass-extinction. Assessing species performance and susceptibilities to decline is essential to comprehend and reverse this trend. Yet it is challenging, given difficulties associated with quantifying individual and population processes that are variable across time, space, and life-stages. We describe a new approach to estimating and comparing species performances that combines empirical data, a novel theoretical consideration of population dynamics, and modern statistics. Our approach allows for a more realistic continuous representation of individual performances along development stages while taking into account non-linearity, and natural variability as captured by spatio-temporally replicated observations. We illustrate its application in a coral meta-assemblage composed of populations of the three major reef-building taxa Acropora, Pocillopora, Porites. Using a unique set of highly replicated observations of individual coral dynamics under various environmental conditions, we show how taxa differ in their investment in recruitment and size-specific aptitude for growth and survival, notably through different use of clonal shrinkage, fragmentation, fission, and fusion processes. Our results reveal contrasting life-history trade-offs among taxa which, along with differing patterns of density-dependent recruitment, modulate species responses to decline. These differences in coral life history traits reflect opposing life-strategies, imply regulation at differing life-stages, and explain divergence in species trajectories. Our findings indicate a high potential for resilience in Pocillopora and Porites populations, thanks respectively to a sustained recruitment that promotes demographic elasticity through replacement of individuals, and a steady resistance to mortality which confers persistence through lingering of individuals. Resilience in Acropora appears more arbitrary, given high susceptibility to perturbations and dependency of recruitment on presence of established local populations. We identify management actions that can complement Acropora's life history and benefit recovery of its populations following mortality events. Our regression-modelling approach to quantifying and comparing species performances in different population processes is applicable to all taxa, as illustrated even those with complex clonal life histories, and can be implemented at wide spatio-temporal and taxonomic coverage. It can promote more accurate representation of species dynamics in both descriptive and predictive modelling approaches. The semi-parametric contrast curve method we develop facilitates comparing response variables along continuous explicative metrics while accounting for multiple sources of complexity in empirical data. It should widely benefit investigations in ecology and quantitative science.

Incorporating phosphorus cycling into global modeling efforts: a worthwhile, tractable endeavor.

324 I. 324 II. 325 III. 326 IV. 327 328 References 328 SUMMARY: Myriad field, laboratory, and modeling studies show that nutrient availability plays a fundamental role in regulating CO2 exchange between the Earth's biosphere and atmosphere, and in determining how carbon pools and fluxes respond to climatic change. Accordingly, global models that incorporate coupled climate-carbon cycle feedbacks made a significant advance with the introduction of a prognostic nitrogen cycle. Here we propose that incorporating phosphorus cycling represents an important next step in coupled climate-carbon cycling model development, particularly for lowland tropical forests where phosphorus availability is often presumed to limit primary production. We highlight challenges to including phosphorus in modeling efforts and provide suggestions for how to move forward.

A Multi-Scale Fuzzy Spatial Analysis Framework for Large Data Based on IT2 FS

The geographical world is an intricate system that comprises the interaction of the Earth's atmosphere, hydrosphere, biosphere, lithosphere, and pedosphere. Existing technologies and systems can only store, represent, and analyze crisp or type-I fuzzy spatial data and obtain spatial knowledge on several discrete scales. However, these technologies are limited to multi-scale and high-order vagueness spatial data representation and analysis, particularly regarding the representation and acquisition of multi-scale knowledge. In this paper, the uncertainty in geographic information systems (GISs) and existing problems in classical spatial analysis methods are summarized. Innovative concepts, such as the scale aggregation model and scale polymorphism, are proposed. A multi-scale fuzzy spatial analysis framework based on an interval type-II fuzzy set is introduced, and critical points are highlighted, such as an interval type-II fuzzy geographical object model (the boundary model and metric methods for geometric properties), direction relations, topological relations, and overlap methods. An actual case based on a multi-scale regional debris-flow hazard assessment is used to confirm the validity of the theory proposed in this paper.

Reduction of the temperature sensitivity of Halomonas hydrothermalis by iron starvation combined with microaerobic conditions.

The limits to biological processes on Earth are determined by physicochemical parameters, such as extremes of temperature and low water availability. Research into microbial extremophiles has enhanced our understanding of the biophysical boundaries which define the biosphere. However, there remains a paucity of information on the degree to which rates of microbial multiplication within extreme environments are determined by the availability of specific chemical elements. Here, we show that iron availability and the composition of the gaseous phase (aerobic versus microaerobic) determine the susceptibility of a marine bacterium, Halomonas hydrothermalis, to suboptimal and elevated temperature and salinity by impacting rates of cell division (but not viability). In particular, iron starvation combined with microaerobic conditions (5% [vol/vol] O2, 10% [vol/vol] CO2, reduced pH) reduced sensitivity to temperature across the 13°C range tested. These data demonstrate that nutrient limitation interacts with physicochemical parameters to determine biological permissiveness for extreme environments. The interplay between resource availability and stress tolerance, therefore, may shape the distribution and ecology of microorganisms within Earth's biosphere.

Heterogeneous redox conditions and a shallow chemocline in the Mesoproterozoic ocean: Evidence from carbon–sulfur–iron relationships

Oxygenation of Earth's oceans in the Proterozoic was a protracted process that began prior to the Great Oxidation Event (GOE) and culminated in deep ocean ventilation following Neoproterozoic glacial episodes, with both of these major thresholds accompanied by profound changes in the evolution of Earth's biosphere. Our understanding of the redox structure of Mesoproterozoic oceans, however, is considerably less certain. Limited proxy investigations of oceanic redox in the Mesoproterozoic have focused largely on early Mesoproterozoic shelf to basinal settings, with comparatively little attention paid to epeiric sea environments that dominate the late Mesoproterozoic sedimentary record. Here we report multi-proxy shale redox data from epicratonic and pericratonic environments of the 1.1Ga Atar and El Mreiti Groups, Taoudeni Basin, Mauritania. These strata were deposited across the West African craton during global sea level highstand, and provide insight into the redox structure of Mesoproterozoic epeiric seas. Iron speciation, pyrite sulfur isotope, and trace metal concentration data suggest a shallow chemocline and highly heterogeneous redox conditions, with fundamental heterogeneities in sulfate concentration and the extent and persistence of euxinia between onshore and offshore environments. We suggest that a protracted increase in biospheric oxygenation in the late Mesoproterozoic was accompanied by unstable and heterogeneous redox conditions in shallow, nearshore areas, contributing to the fragmentary pattern of early eukaryotic evolution and diversification.

Modeling of abiotic ATP synthesis in the context of problems of early biosphere evolution

The pathway of adenosine triphosphate (ATP) synthesis in living organisms consists of two autonomous stages; this must be taken into account during the design and analysis of chemical models of the abiogenesis of this key participant of metabolic processes. The first stage is construction of an adenine heterocycle linked to a ribose-5-phosphate molecule to yield AMP, while the following stage is the attachment of phosphoryl residues to the nucleotide molecule by macroergic phosphoanhydride bonds. Involvement of the same set of precursor molecules in both de novo biosynthesis of AMP and abiogenesis of this nucleotide is a very important issue for the analysis of metabolic pathways. Photochemical matrix systems that convert light energy into macroergic bond energy are functional prototypes of photosynthetic phosphorylation; they are of special interest for the construction of abiotic phosphorylation models. Interaction of substrates with a purely mineral matrix (montmorillonite particles) under UV irradiation resulted in the formation of ATP from ADP and orthophosphate. Micro-and nanostructures that formed upon the interaction of the mineral component (sodium polysilicate) with an abiogenic organic pigment (a flavin conjugate with a random amino acid polymer) exhibited phosphorylating activity as well when irradiated with visible light. The properties of AMP and ATP abiosynthesis models investigated are in good accordance with the current views on the environmental conditions of the ancient Earth; evident structural differences exist between these models and the biosynthetic systems in modern organisms.

Rapid exchange between atmospheric CO2 and carbonate anion intercalated within magnesium rich layered double hydroxide.

The carbon cycle, by which carbon atoms circulate between atmosphere, oceans, lithosphere, and the biosphere of Earth, is a current hot research topic. The carbon cycle occurring in the lithosphere (e.g., sedimentary carbonates) is based on weathering and metamorphic events so that its processes are considered to occur on the geological time scale (i.e., over millions of years). In contrast, we have recently reported that carbonate anions intercalated within a hydrotalcite (Mg0.75Al0.25(OH)2(CO3)0.125·yH2O), a class of a layered double hydroxide (LDH), are dynamically exchanging on time scale of hours with atmospheric CO2 under ambient conditions. (Ishihara et al., J. Am. Chem. Soc. 2013, 135, 18040-18043). The use of (13)C-labeling enabled monitoring by infrared spectroscopy of the dynamic exchange between the initially intercalated (13)C-labeled carbonate anions and carbonate anions derived from atmospheric CO2. In this article, we report the significant influence of Mg/Al ratio of LDH on the carbonate anion exchange dynamics. Of three LDHs of various Mg/Al ratios of 2, 3, or 4, magnesium-rich LDH (i.e., Mg/Al ratio = 4) underwent extremely rapid exchange of carbonate anions, and most of the initially intercalated carbonate anions were replaced with carbonate anions derived from atmospheric CO2 within 30 min. Detailed investigations by using infrared spectroscopy, scanning electron microscopy, powder X-ray diffraction, elemental analysis, adsorption, thermogravimetric analysis, and solid-state NMR revealed that magnesium rich LDH has chemical and structural features that promote the exchange of carbonate anions. Our results indicate that the unique interactions between LDH and CO2 can be optimized simply by varying the chemical composition of LDH, implying that LDH is a promising material for CO2 storage and/or separation.

Late Proterozoic–Early Phanerozoic ‘Taphonomic Windows’: The Environmental and Temporal Distribution of Recurrent Modes of Exceptional Preservation

Exceptional biotas—those in which the non-biomineralized tissues of organisms are preserved—are an important record of the evolutionary biology of the late Neoproterozoic—early Phanerozoic interval. Most of these biotas exhibit one of four modes of preservation: preservation of either 1) internal and external detail (Doushantuo-type preservation) or, 2) external cuticles (Orsten-type preservation) in calcium phosphate; 3) coating in pyrite films and infills (Beecher's Bed-type preservation); and 4) preservation of organic remains (Burgess Shale-type preservation). The global environmental and temporal distribution of each mode of preservation is reasonably well constrained, but not why these taphonomic windows existed when they did. The late Neoproterozoic – early Phanerozoic interval is characterized by complex, interlinked, physical, geochemical and biological changes to the Earth's biosphere and geosphere. The changing ecology of marine environments (from matground to mixgrounds: the ‘Agronomic Revolution’) occurred via an intermediate phase of stiffened, but not microbially bound sediments that extended the interval over which exceptional preservation occurred. Prolonged eustatic sea-level rise across flat-lying continental platforms ensured environments conducive to exceptional preservation were developed and, critically, sustained over large contiguous areas. During this, regolith on continental surfaces was recycled, providing an integral source of sediment and ions relevant to mineral authigenesis. Superimposed on these broad-scale changes are specific drivers that controlled the duration of individual taphonomic windows; elucidating these requires a better understanding of the environmental context and diagenetic history of fossiliferous successions at the intra-basinal scale.

Multiplication of microbes below 0.690 water activity: implications for terrestrial and extraterrestrial life.

Since a key requirement of known life forms is available water (water activity; aw ), recent searches for signatures of past life in terrestrial and extraterrestrial environments have targeted places known to have contained significant quantities of biologically available water. However, early life on Earth inhabited high-salt environments, suggesting an ability to withstand low water-activity. The lower limit of water activity that enables cell division appears to be ∼ 0.605 which, until now, was only known to be exhibited by a single eukaryote, the sugar-tolerant, fungal xerophile Xeromyces bisporus. The first forms of life on Earth were, though, prokaryotic. Recent evidence now indicates that some halophilic Archaea and Bacteria have water-activity limits more or less equal to those of X. bisporus. We discuss water activity in relation to the limits of Earth's present-day biosphere; the possibility of microbial multiplication by utilizing water from thin, aqueous films or non-liquid sources; whether prokaryotes were the first organisms able to multiply close to the 0.605-aw limit; and whether extraterrestrial aqueous milieux of ≥ 0.605 aw can resemble fertile microbial habitats found on Earth.

Physiosemiosis as an Influence of Signs

Abstract It took most of the 20th century fully to establish semiotics as a thematic study of the role and action of signs not only in human culture and life but also in the whole environment that human animals share with all the other life forms that make up the biosphere of planet earth. In the early 20th century investigators were inclined to restrict the action of signs to the realm of human culture and psychology, consistent with the ideas of modern philosophy that severely separates the world of humans from its surroundings supposed as “unknowable” in itself. This idealistic ne plus ultra was definitively transgressed and shattered by the collegial work of Thomas A. Sebeok, who not only established the framework for a “global semiotics” but also demonstrated unequivocally that the whole world of living things (the “biosphere”) cannot exist independently of the action of signs. As Sebeok put it, “semiosis is coextensive with life”. But there remains even so the further question: “Is life coextensive with semiosis?” For, from the demonstration that semiosis is essential for the existence of life, it does not follow that the existence of life is essential for there to be semiosis. It is this last proposition - wrongly taken by many (or most) proponents of biosemiotics today to be a logical consequent of the conclusion that life in its full extent depends upon semiosis - that I examine here: the probability that semiosis not only surrounds life but pre-existed living things, and indeed shaped the universe so as to make living things possible in the first place.

Snow surface microbiome on the High Antarctic Plateau (DOME C).

The cryosphere is an integral part of the global climate system and one of the major habitable ecosystems of Earth's biosphere. These permanently frozen environments harbor diverse, viable and metabolically active microbial populations that represent almost all the major phylogenetic groups. In this study, we investigated the microbial diversity in the surface snow surrounding the Concordia Research Station on the High Antarctic Plateau through a polyphasic approach, including direct prokaryotic quantification by flow cytometry and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and phylogenetic identification by 16S RNA gene clone library sequencing and 454 16S amplicon pyrosequencing. Although the microbial abundance was low (<103 cells/ml of snowmelt), concordant results were obtained with the different techniques. The microbial community was mainly composed of members of the Alpha-proteobacteria class (e.g. Kiloniellaceae and Rhodobacteraceae), which is one of the most well-represented bacterial groups in marine habitats, Bacteroidetes (e.g. Cryomorphaceae and Flavobacteriaceae) and Cyanobacteria. Based on our results, polar microorganisms could not only be considered as deposited airborne particles, but as an active component of the snowpack ecology of the High Antarctic Plateau.

Is there overshoot of planetary limits? New indicators of human appropriation of the global biogeochemical cycles relative to their regenerative capacity based on ‘ecotime’ analysis

The global biogeochemical cycles are recognised as extremely important processes operating within the Earth's (geo)biosphere. However, there are currently few methods available through which we can understand and communicate humanity's dependence on these cycles. This paper presents a novel method, based on input–output analysis, for deriving a suite of indicators describing the level at which the global economy, through its transformation of useful resources (i.e. raw materials) into residuals (i.e. wastes, pollutants, emissions), is appropriating biogeochemical processes. Furthermore, significant insight into the scale of the global economic system is gained by comparing the rate of human appropriation of biogeochemical cycling with that of the biosphere's regenerative capacity. In order to calculate these indicators, we create a new concept of ‘ecotime’, defined as the average biogeochemical cycling time available for matter held within differing types of environmental commodities (e.g. carbon dioxide, plants, fossil fuels) to reach biogeochemical processes under consideration. Resources used by the global economy generally have long ecotimes, while the residuals produced by economic activities generally have short ecotimes. Applying our method to an extensive database encompassing the key biogeochemical cycles, it is found that humans are placing significant pressure on these cycles.

Superoxide Dismutases and Superoxide Reductases

Superoxide, O2•–, is formed in all living organisms that come in contact with air, and, depending upon its biological context, it may act as a signaling agent, a toxic species, or a harmless intermediate that decomposes spontaneously. Its levels are limited in vivo by two different types of enzymes, superoxide reductase (SOR) and superoxide dismutase (SOD). Although superoxide has long been an important factor in evolution, it was not so when life first emerged on Earth at least 3.5 billion years ago. At that time, the early biosphere was highly reducing and lacking in any significant concentrations of dioxygen (O2), very different from what it is today. Consequently, there was little or no O2•– and therefore no reason for SOR or SOD enzymes to evolve. Instead, the history of biological O2•– probably commences somewhere around 2.4 billion years ago, when the biosphere started to experience what has been termed the “Great Oxidation Event”, a transformation driven by the increase in O2 levels, formed by cyanobacteria as a product of oxygenic photosynthesis.1 The rise of O2 on Earth caused a reshaping of existing metabolic pathways, and it triggered the development of new ones.2 Its appearance led to the formation of the so-called “reactive oxygen species” (ROS), for example, superoxide, hydrogen peroxide, and hydroxyl radical, and to a need for antioxidant enzymes and other antioxidant systems to protect against the growing levels of oxidative damage to living systems. Dioxygen is a powerful four-electron oxidizing agent, and the product of this reduction is water. 1 When O2 is reduced in four sequential one-electron steps, the intermediates formed are the three major ROS, that is, O2•–, H2O2, and HO•. 2 3 4 5 Each of these intermediates is a potent oxidizing agent. The consequences of their presence to early life must have been an enormous evolutionary challenge. In the case of superoxide, we find the SOD and SOR enzymes to be widely distributed throughout current living organisms, both aerobic and anaerobic, suggesting that, from the start of the rise of O2 on Earth, the chemistry of superoxide has been an important factor during evolution. The SORs and three very different types of SOD enzymes are redox-active metalloenzymes that have evolved entirely independently from one another for the purpose of lowering superoxide concentrations. SORs catalyze the one-electron reduction of O2•– to give H2O2, a reaction requiring two protons per superoxide reacted as well as an external reductant to provide the electron (eq 6). SODs catalyze the disproportionation of superoxide to give O2 and H2O2, a reaction requiring one proton per superoxide reacted, but no external reductant (eq 7). 6 7 All of the SOR enzymes contain only iron, while the three types of SODs are the nickel-containing SODs (NiSOD), the iron- or manganese-containing SODs (FeSOD and MnSOD), and the copper- and zinc-containing SODs (CuZnSOD). Although the structures and other properties of these four types of metalloenzymes are quite different, they all share several characteristics, including the ability to react rapidly and selectively with the small anionic substrate O2•–. Consequently, there are some striking similarities between these otherwise dissimilar enzymes, many of which can be explained by considering the nature of the chemical reactivity of O2•– (see below). Numerous valuable reviews describing the SOD and SOR enzymes have appeared over the years, but few have covered and compared all four classes of these enzymes, as we attempt to do here. Thus, the purpose of this Review is to describe, compare, and contrast the properties of the SOR and the four SOD enzymes; to summarize what is known about their evolutionary pathways; and to analyze the properties of these enzymes in light of what is known of the inherent chemical reactivity of superoxide.

GeoChip 4: a functional gene‐array‐based high‐throughput environmental technology for microbial community analysis

Micro-organisms play critical roles in many important biogeochemical processes in the Earth's biosphere. However, understanding and characterizing the functional capacity of microbial communities are still difficult due to the extremely diverse and often uncultivable nature of most micro-organisms. In this study, we developed a new functional gene array, GeoChip 4, for analysing the functional diversity, composition, structure, metabolic potential/activity and dynamics of microbial communities. GeoChip 4 contained approximately 82000 probes covering 141995 coding sequences from 410 functional gene families related to microbial carbon (C), nitrogen (N), sulphur (S), and phosphorus (P) cycling, energy metabolism, antibiotic resistance, metal resistance/reduction, organic remediation, stress responses, bacteriophage and virulence. A total of 173 archaeal, 4138 bacterial, 404 eukaryotic and 252 viral strains were targeted, providing the ability to analyse targeted functional gene families of micro-organisms included in all four domains. Experimental assessment using different amounts of DNA suggested that as little as 500ng environmental DNA was required for good hybridization, and the signal intensities detected were well correlated with the DNA amount used. GeoChip 4 was then applied to study the effect of long-term warming on soil microbial communities at a Central Oklahoma site, with results indicating that microbial communities respond to long-term warming by enriching carbon degradation, nutrient cycling (nitrogen and phosphorous) and stress response gene families. To the best of our knowledge, GeoChip 4 is the most comprehensive functional gene array for microbial community analysis.