scholarly journals Temporal variation of planetary iron as a driver of evolution

2021 ◽  
Vol 118 (51) ◽  
pp. e2109865118
Author(s):  
Jon Wade ◽  
David J. Byrne ◽  
Chris J. Ballentine ◽  
Hal Drakesmith
Keyword(s):  
Iron Acquisition ◽  
Atmospheric Oxygen ◽  
Genetic Selection ◽  
Transition Element ◽  
Global Scale ◽  
Biochemical Properties ◽  
Element Distribution ◽  
Iron Bioavailability ◽  
Geological Time ◽  
Core Mass

Iron is an irreplaceable component of proteins and enzyme systems required for life. This need for iron is a well-characterized evolutionary mechanism for genetic selection. However, there is limited consideration of how iron bioavailability, initially determined by planetary accretion but fluctuating considerably at global scale over geological time frames, has shaped the biosphere. We describe influences of iron on planetary habitability from formation events >4 Gya and initiation of biochemistry from geochemistry through oxygenation of the atmosphere to current host–pathogen dynamics. By determining the iron and transition element distribution within the terrestrial planets, planetary core formation is a constraint on both the crustal composition and the longevity of surface water, hence a planet’s habitability. As such, stellar compositions, combined with metallic core-mass fraction, may be an observable characteristic of exoplanets that relates to their ability to support life. On Earth, the stepwise rise of atmospheric oxygen effectively removed gigatons of soluble ferrous iron from habitats, generating evolutionary pressures. Phagocytic, infectious, and symbiotic behaviors, dating from around the Great Oxygenation Event, refocused iron acquisition onto biotic sources, while eukaryotic multicellularity allows iron recycling within an organism. These developments allow life to more efficiently utilize a scarce but vital nutrient. Initiation of terrestrial life benefitted from the biochemical properties of abundant mantle/crustal iron, but the subsequent loss of iron bioavailability may have been an equally important driver of compensatory diversity. This latter concept may have relevance for the predicted future increase in iron deficiency across the food chain caused by elevated atmospheric CO2.

scholarly journals Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean

2021 ◽  
Author(s):  
Lauren E. Manck ◽  
Jiwoon Park ◽  
Benjamin J. Tully ◽  
Alfonso M. Poire ◽  
Randelle M. Bundy ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Iron Acquisition ◽  
Biogeochemical Cycling ◽  
Iron Bioavailability ◽  
Siderophore Production ◽  
Global Ocean ◽  
The North ◽  
The North Pacific ◽  
Alteromonas Macleodii

AbstractIt is now widely accepted that siderophores play a role in marine iron biogeochemical cycling. However, the mechanisms by which siderophores affect the availability of iron from specific sources and the resulting significance of these processes on iron biogeochemical cycling as a whole have remained largely untested. In this study, we develop a model system for testing the effects of siderophore production on iron bioavailability using the marine copiotroph Alteromonas macleodii ATCC 27126. Through the generation of the knockout cell line ΔasbB::kmr, which lacks siderophore biosynthetic capabilities, we demonstrate that the production of the siderophore petrobactin enables the acquisition of iron from mineral sources and weaker iron-ligand complexes. Notably, the utilization of lithogenic iron, such as that from atmospheric dust, indicates a significant role for siderophores in the incorporation of new iron into marine systems. We have also detected petrobactin, a photoreactive siderophore, directly from seawater in the mid-latitudes of the North Pacific and have identified the biosynthetic pathway for petrobactin in bacterial metagenome-assembled genomes widely distributed across the global ocean. Together, these results improve our mechanistic understanding of the role of siderophore production in iron biogeochemical cycling in the marine environment wherein iron speciation, bioavailability, and residence time can be directly influenced by microbial activities.

scholarly journals The origins of modern biodiversity on land

2010 ◽  
Vol 365 (1558) ◽  
pp. 3667-3679 ◽  
Author(s):  
Michael J. Benton
Keyword(s):  
Regional Scale ◽  
Global Scale ◽  
Scale Model ◽  
Time Range ◽  
Geological Time ◽  
New Methods ◽  
Evolution Of Life ◽  
History Of ◽  
Extinction Events ◽  
Mass Extinction Events

Comparative studies of large phylogenies of living and extinct groups have shown that most biodiversity arises from a small number of highly species-rich clades. To understand biodiversity, it is important to examine the history of these clades on geological time scales. This is part of a distinct ‘phylogenetic expansion’ view of macroevolution, and contrasts with the alternative, non-phylogenetic ‘equilibrium’ approach to the history of biodiversity. The latter viewpoint focuses on density-dependent models in which all life is described by a single global-scale model, and a case is made here that this approach may be less successful at representing the shape of the evolution of life than the phylogenetic expansion approach. The terrestrial fossil record is patchy, but is adequate for coarse-scale studies of groups such as vertebrates that possess fossilizable hard parts. New methods in phylogenetic analysis, morphometrics and the study of exceptional biotas allow new approaches. Models for diversity regulation through time range from the entirely biotic to the entirely physical, with many intermediates. Tetrapod diversity has risen as a result of the expansion of ecospace, rather than niche subdivision or regional-scale endemicity resulting from continental break-up. Tetrapod communities on land have been remarkably stable and have changed only when there was a revolution in floras (such as the demise of the Carboniferous coal forests, or the Cretaceous radiation of angiosperms) or following particularly severe mass extinction events, such as that at the end of the Permian.

scholarly journals Palette of Luciferases: Natural Biotools for New Applications in Biomedicine

Acta Naturae ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 15-27
Author(s):  
A. A. Kotlobay ◽  
Z. M. Kaskova ◽  
I. V. Yampolsky
Keyword(s):  
Atmospheric Oxygen ◽  
Biochemical Properties ◽  
Quantum Yields ◽  
External Irradiation ◽  
Low Molecular Weight ◽  
Non Invasive ◽  
Enzyme Thermostability ◽  
Highly Sensitive ◽  
New Applications ◽  
Optimal Ph

Optoanalytical methods based on using genetically encoded bioluminescent enzymes,luciferases, allow one to obtain highly sensitive signals, are non-invasive, and require no external irradiation. Bioluminescence is based on the chemical reaction of oxidation of a low-molecular-weight substrate (luciferin) by atmospheric oxygen, which is catalyzed by an enzyme (luciferase). Relaxation of the luciferin oxidation product from its excited state is accompanied by a release of a quantum of light, which can be detected as an analytical signal.The ability to express luciferase genes in various heterological systems and high quantum yields of luminescence reactions have made these tools rather popular in biology and medicine. Amongseveral naturally available luciferases, a few have been found to be useful for practicalapplication. Luciferase size, the wavelength of its luminescence maximum, enzyme thermostability, optimal pH of the reaction, and the need for cofactors areparameters that may differ for luciferases from different groups of organisms, and this fact directly affects the choice of the application area for each enzyme. It is quite important to overview the whole range of currently available luciferases based ontheir biochemical properties before choosing one bioluminescent probe suitable for a specific application.

scholarly journals Reduction-dependent siderophore assimilation in a model pennate diatom

2019 ◽  
Vol 116 (47) ◽  
pp. 23609-23617 ◽  
Author(s):  
Tyler H. Coale ◽  
Mark Moosburner ◽  
Aleš Horák ◽  
Miroslav Oborník ◽  
Katherine A. Barbeau ◽  
...  
Keyword(s):  
Iron Uptake ◽  
Iron Acquisition ◽  
Close Association ◽  
Iron Bioavailability ◽  
Trophic Levels ◽  
Receptor Protein ◽  
Pennate Diatom ◽  
Surface Ocean ◽  
Specific Proteins ◽  
Genetic Techniques

Iron uptake by diatoms is a biochemical process with global biogeochemical implications. In large regions of the surface ocean diatoms are both responsible for the majority of primary production and frequently experiencing iron limitation of growth. The strategies used by these phytoplankton to extract iron from seawater constrain carbon flux into higher trophic levels and sequestration into sediments. In this study we use reverse genetic techniques to target putative iron-acquisition genes in the model pennate diatom Phaeodactylum tricornutum. We describe components of a reduction-dependent siderophore acquisition pathway that relies on a bacterial-derived receptor protein and provides a viable alternative to inorganic iron uptake under certain conditions. This form of iron uptake entails a close association between diatoms and siderophore-producing organisms during low-iron conditions. Homologs of these proteins are found distributed across diatom lineages, suggesting the significance of siderophore utilization by diatoms in the marine environment. Evaluation of specific proteins enables us to confirm independent iron-acquisition pathways in diatoms and characterize their preferred substrates. These findings refine our mechanistic understanding of the multiple iron-uptake systems used by diatoms and help us better predict the influence of iron speciation on taxa-specific iron bioavailability.

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

2019 ◽  
Vol 116 (38) ◽  
pp. 18854-18859 ◽  
Author(s):  
He Liu ◽  
Robert E. Zartman ◽  
Trevor R. Ireland ◽  
Wei-dong Sun
Keyword(s):  
Oceanic Crust ◽  
Sea Water ◽  
Atmospheric Oxygen ◽  
Sharp Decrease ◽  
Temporal Variations ◽  
Global Scale ◽  
Significant Rise ◽  
Water Soluble ◽  
Igneous Rocks ◽  
Major Step

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

scholarly journals eSCAPE: Regional to Global Scale Landscape Evolution Model v2.0

2019 ◽  
Author(s):  
Tristan Salles
Keyword(s):  
Landscape Evolution ◽  
Iterative Algorithms ◽  
Sedimentary Basins ◽  
Global Scale ◽  
Evolution Model ◽  
Mathematical Representation ◽  
Stream Power ◽  
Geological Time ◽  
Surface Evolution ◽  
Source To Sink

Abstract. eSCAPE is a Python-based landscape evolution model that simulates over geological time (1) the dynamic of the landscape, (2) the transport of sediment from source to sink, and (3) continental and marine sedimentary basins formation under different climatic and tectonic conditions. eSCAPE is open-source, cross-platform, distributed under the GPLv3 license and available on GitHub (escape-model.github.io). Simulated processes rely on a simplified mathematical representation of landscape processes – the stream power and creep laws – to compute Earth's surface evolution by rivers and hillslope transport. The main difference with previous models is in the underlying numerical formulation of the mathematical equations. The approach is based on a series of implicit iterative algorithms defined in matrix form to calculate both drainage area from multiple flow directions and erosion/deposition processes. eSCAPE relies on PETSc parallel library to solve these matrix systems. Along with the description of the algorithms, examples are provided and illustrate the model current capabilities and limitations. eSCAPE is the first landscape evolution model able to simulate processes at global scale and is primarily designed to address problems on large unstructured grids (several millions of nodes).

What, if anything, are mass extinctions?

1989 ◽  
Vol 325 (1228) ◽  
pp. 253-261 ◽  
Keyword(s):  
Organic Matter ◽  
Mass Extinction ◽  
Atmospheric Oxygen ◽  
World Ocean ◽  
Nutrient Deficiency ◽  
Late Eocene ◽  
Global Ocean ◽  
Mass Extinctions ◽  
Geological Time ◽  
Sea Bottom

Many phenomena that have traditionally been called ‘mass extinctions’ are in fact clusters of extinction episodes roughly associated in geological time. This is the case with the latest Ordovician, late Devonian, mid-Cretaceous, latest Cretaceous and Late Eocene-Oligocene extinctions. Several of these clusters are caused, each episode by a different causal factor. Such mass extinctions are then due to the coincidence of various processes in the environment, and they can hardly be considered as individual events. The latest Permian mass extinction, however, is caused by a single process that affected the global ocean-atmosphere system. In the late Permian, the world ocean was full of deposits rich in organic matter, which enhanced nutrient recycling. After oxygen was brought to the sea floor (by whatever process), nutrients began to sink to the sea-bottom, and the resulting nutrient deficiency must have caused mass extinction in the sea. Oxidation of huge amounts of organic matter and associated sediments at the sea bottom must have drawn oxygen from the atmosphere, and the resulting fall in atmospheric oxygen must have contributed to extinctions on land.

scholarly journals Energy metabolism among eukaryotic anaerobes in light of Proterozoic ocean chemistry

2008 ◽  
Vol 363 (1504) ◽  
pp. 2717-2729 ◽  
Author(s):  
Marek Mentel ◽  
William Martin
Keyword(s):  
Energy Metabolism ◽  
Alternative Hypothesis ◽  
Atmospheric Oxygen ◽  
Global Scale ◽  
Evolutionary Significance ◽  
Significant Finding ◽  
Eukaryotic Evolution ◽  
Important Advance ◽  
The Earth ◽  
Ocean Chemistry

Recent years have witnessed major upheavals in views about early eukaryotic evolution. One very significant finding was that mitochondria, including hydrogenosomes and the newly discovered mitosomes, are just as ubiquitous and defining among eukaryotes as the nucleus itself. A second important advance concerns the readjustment, still in progress, about phylogenetic relationships among eukaryotic groups and the roughly six new eukaryotic supergroups that are currently at the focus of much attention. From the standpoint of energy metabolism (the biochemical means through which eukaryotes gain their ATP, thereby enabling any and all evolution of other traits), understanding of mitochondria among eukaryotic anaerobes has improved. The mainstream formulations of endosymbiotic theory did not predict the ubiquity of mitochondria among anaerobic eukaryotes, while an alternative hypothesis that specifically addressed the evolutionary origin of energy metabolism among eukaryotic anaerobes did. Those developments in biology have been paralleled by a similar upheaval in the Earth sciences regarding views about the prevalence of oxygen in the oceans during the Proterozoic (the time from ca 2.5 to 0.6 Ga ago). The new model of Proterozoic ocean chemistry indicates that the oceans were anoxic and sulphidic during most of the Proterozoic. Its proponents suggest the underlying geochemical mechanism to entail the weathering of continental sulphides by atmospheric oxygen to sulphate, which was carried into the oceans as sulphate, fuelling marine sulphate reducers (anaerobic, hydrogen sulphide-producing prokaryotes) on a global scale. Taken together, these two mutually compatible developments in biology and geology underscore the evolutionary significance of oxygen-independent ATP-generating pathways in mitochondria, including those of various metazoan groups, as a watermark of the environments within which eukaryotes arose and diversified into their major lineages.

scholarly journals Conservation and Loss of a Putative Iron Utilization Gene Cluster among Genotypes of Aspergillus flavus

2021 ◽  
Vol 9 (1) ◽  
pp. 137
Author(s):  
Bishwo N. Adhikari ◽  
Kenneth A. Callicott ◽  
Peter J. Cotty
Keyword(s):  
Gene Cluster ◽  
Aspergillus Flavus ◽  
Iron Uptake ◽  
Ferric Iron ◽  
Iron Acquisition ◽  
Atmospheric Oxygen ◽  
Iron Availability ◽  
Specific Loss ◽  
Complete Deletion ◽  
Iron Utilization

Iron is an essential component for growth and development. Despite relative abundance in the environment, bioavailability of iron is limited due to oxidation by atmospheric oxygen into insoluble ferric iron. Filamentous fungi have developed diverse pathways to uptake and use iron. In the current study, a putative iron utilization gene cluster (IUC) in Aspergillus flavus was identified and characterized. Gene analyses indicate A. flavus may use reductive as well as siderophore-mediated iron uptake and utilization pathways. The ferroxidation and iron permeation process, in which iron transport depends on the coupling of these two activities, mediates the reductive pathway. The IUC identified in this work includes six genes and is located in a highly polymorphic region of the genome. Diversity among A. flavus genotypes is manifested in the structure of the IUC, which ranged from complete deletion to a region disabled by multiple indels. Molecular profiling of A. flavus populations suggests lineage-specific loss of IUC. The observed variation among A. flavus genotypes in iron utilization and the lineage-specific loss of the iron utilization genes in several A. flavus clonal lineages provide insight on evolution of iron acquisition and utilization within Aspergillus section Flavi. The potential divergence in capacity to acquire iron should be taken into account when selecting A. flavus active ingredients for biocontrol in niches where climate change may alter iron availability.

scholarly journals Possible link between Earth’s rotation rate and oxygenation

2021 ◽  
Author(s):  
J. M. Klatt ◽  
A. Chennu ◽  
B. K. Arbic ◽  
B. A. Biddanda ◽  
G. J. Dick
Keyword(s):  
Metabolic Regulation ◽  
Atmospheric Oxygen ◽  
Dynamic Modelling ◽  
Low Oxygen ◽  
Geological Time ◽  
Net Productivity ◽  
Carbon Burial ◽  
Organic Carbon Burial ◽  
Solute Fluxes ◽  
Benthic Ecosystems

AbstractThe biotic and abiotic controls on major shifts in atmospheric oxygen and the persistence of low-oxygen periods over a majority of Earth’s history remain under debate. Explanations of Earth’s stepwise pattern of oxygenation have mostly neglected the effect of changing diel illumination dynamics linked to daylength, which has increased through geological time due to Earth’s rotational deceleration caused by tidal friction. Here we used microsensor measurements and dynamic modelling of interfacial solute fluxes in cyanobacterial mats to investigate the effect of changing daylength on Precambrian benthic ecosystems. Simulated increases in daylength across Earth’s historical range boosted the diel benthic oxygen export, even when the gross photosynthetic production remained constant. This fundamental relationship between net productivity and daylength emerges from the interaction of diffusive mass transfer and diel illumination dynamics, and is amplified by metabolic regulation and microbial behaviour. We found that the resultant daylength-driven surplus organic carbon burial could have shaped the increase in atmospheric oxygen that occurred during the Great and Neoproterozoic Oxidation Events. Our suggested mechanism, which links the coinciding increases in daylength and atmospheric oxygen via enhanced net productivity, reveals a possible contribution of planetary mechanics to the evolution of Earth’s biology and geochemistry.

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