The Great Oxidation Event preceded a Paleoproterozoic “snowball Earth”

Warke, Matthew R.; Rocco, Tommaso Di; Zerkle, Aubrey L.; Lepland, Aivo; Prave, Anthony R.; Martin, Adam P.; Ueno, Yuichiro; Condon, Daniel J.; Claire, Mark

doi:10.1073/pnas.2003090117

Cited by 116 publications

(76 citation statements)

References 55 publications

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“…Unlike other elements with complex redox chemistry, such as Fe or S, Li has straightforward redox chemistry and relatively smaller associated networks. We emphasize that dragon is designed to analyze complex and larger mineral-chemistry networks with complex redox changes, as associated with oxygenation events for example (Scott et al, 2008;Och and Shields-Zhou, 2012;Sahoo et al, 2012;Warke et al, 2020), but we focus on the simpler Li network here to clearly showcase dragon's functionality.…”

Section: Resultsmentioning

confidence: 99%

“…Finally, dragon's fourth tab "Mineral formation timeline" provides a chronological view of mineral formation scaffolded along geologic eras, including periods of tectonic assembly, oxygenation events in Earth's history (Farquhar et al, 2000;Scott et al, 2008;Och and Shields-Zhou, 2012;Sahoo et al, 2012;Luo et al, 2016;Warke et al, 2020), and early geochemical evidence for microbial metabolisms (Moore et al, 2017) ( Figure 1D).…”

Section: Analyzing Network In Dragonmentioning

confidence: 99%

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dragon: A New Tool for Exploring Redox Evolution Preserved in the Mineral Record

Spielman

Moore

2020

Front. Earth Sci.

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The flow of energy and elements between the geosphere and biosphere can be traced through changing redox chemistry of Earth's surface. Deep-time trends in the mineral record, including mineral age and elemental composition, reveal a dynamic history of changing redox states and chemical speciation. We present a user-friendly exploratory network analysis platform called dragon (Deep-time Redox Analysis of the Geobiology Ontology Network) to facilitate investigation of the expanding redox chemical network preserved in the mineral record throughout Earth's history and beyond. Given a userindicated focal element or set of focal elements, dragon constructs interactive bipartite networks of minerals and their constituent elements over a specified range in geologic-time using information from the Mineral Evolution Database (https://rruff.info/evolution/). Written in the open-source language R as a Shiny application, dragon launches a browser-based dashboard to explore mineral evolution in deep-time. We demonstrate dragon's utility through examining the mineral chemistry of lithium over deep-time. dragon is freely available from CRAN under a GPL-3 License, with source code and documentation hosted at https://github.com/sjspielman/dragon.

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Section: Resultsmentioning

confidence: 99%

Section: Analyzing Network In Dragonmentioning

confidence: 99%

dragon: A New Tool for Exploring Redox Evolution Preserved in the Mineral Record

Spielman

Moore

2020

Front. Earth Sci.

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“…However, it is currently unclear whether this was a globally synchronous event with estimates for MIF-S disappearance varying from 2.45 to 2.32 Ga due to uncertainties over memory effects caused by oxidative weathering of sulphides and recycling of the MIF signature (Reinhard et al, 2013;Philippot et al, 2018;cf. Torres et al, 2018;Warke et al, 2020b). The MIF-S record has also shown structure within the later Archean that could potentially be used as a future stratigraphic marker (Farquhar et al, 2007;Domagal-Goldman et al, 2008;Halevy et al, 2010;Kurzweil et al, 2013) if the structure is confirmed as a global phenomenon rather than superimposed local signals (see e.g.…”

Section: Archean Eon (C 40 To 245/25 Ga)mentioning

confidence: 99%

“…Although the GOE is sometimes taken to refer to a more prolonged interval of the early Paleoproterozoic, we restrict our usage here to this shorter interval between c. 2.45 to c. 2.32 Ga, with a preference for the earlier age (e.g. Warke et al, 2020b). The GOE has been defined in various ways but in recent years has been presumed to begin when atmospheric oxygen had accumulated sufficiently to prevent the formation and/or preservation of mass independent S-isotope fractionation in sedimentary rocks (Farquhar et al, 2000;Bekker et al, 2004).…”

Section: Archean Eon (C 40 To 245/25 Ga)mentioning

confidence: 99%

Towards a new geological time scale: A template for improved rock-based subdivision of pre-Cryogenian time

Shields¹,

Strachan²,

Porter³

et al. 2022

Preprint

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Four first-order (Hadean, Archean, Proterozoic and Phanerozoic eon) and nine second-order (Paleoarchean, Mesoarchean, Neoarchean, Paleoproterozoic, Mesoproterozoic, Neoproterozoic, Paleozoic, Mesozoic and Cenozoic era) units continue to provide intuitive subdivision of geological time. Major transitions in Earth's tectonic, biological and environmental history occurred at approximately 2.5-2.3, 1.8-1.6, 1.0-0.8 and 0.7-0.5 Ga, and so future rock-based subdivision of pre-Cryogenian time, eventually by use of global stratotypes (GSSPs), will likely require only modest deviation from current chronometric boundaries (GSSAs) at 2.5, 1.6 and 1.0 Ga, respectively. Here we argue that removal of GSSAs could be expedited by establishing event-based concepts and provisional, approximate ages for eon-, era-and period-level subdivisions as soon as practicable, in line with ratification of an Ediacaran GSSP in 2004 and chronostratigraphic definition of the Cryogenian Period at c. 720 Ma in 2012. We also outline the geological basis behind current chronometric divisions, explore how they might differ in any future rock-based scheme, identify where major issues might arise during the transition, and outline where some immediate changes to the present scheme could be easily updated/formalised, as a framework for future GSSP development. In line with these aims, we note that the currently recommended four-fold Archean subdivision has not been formally ratified and agree with previous workers that it could be simplified to an informal threefold subdivision, pending more detailed analysis. Although the ages of period boundaries would inevitably change in a more closely rock-based or chronostratigraphic scheme, we support retention of all currently ratified period names. Existing period names, borrowed from the Greek, were chosen to delimit natural phenomena of global reach. Any new global nomenclature ought to follow this lead for consistency, and so we discourage the use of supercontinent names (e.g. Rodinian, Columbian) and regional phenomena, however exceptional. In this regard, we tentatively suggest that a new period (e.g. the 'Kratian'), could precede the Tonian as the first period of the Neoproterozoic Era and we concur with previous authors that the existing Siderian Period (named for banded iron formations) would fit better as a chronostratigraphically defined period of the terminal Archean. Indeed, all pre-Cryogenian subdivisions will need more conceptual grounding in any future chronostratigraphic scheme. We conclude that improved rock-based division of the Proterozoic Eon would likely comprise a threefold , period-level subdivision of the Paleoproterozoic Era (Oxygenian Rhyacian, Orosirian), a four-fold subdivision of the Mesoproterozoic Era (Statherian, Calymmian, Ectasian, Stenian) and potentially four-fold subdivision of the Neoproterozoic Era (pre-Tonian 'Kratian', Tonian, Cryogenian and Ediacaran). Future refinements towards an improved rockbased pre-Cryogenian geological time scale could be propoosed by new interna...

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“…Accordingly, the Calvin cycle is also named the reductive pentose phosphate cycle. Rubisco evolved from a methionine salvage enzyme [ 12 ] over 2.9 billion years ago [ 13 ], before the great oxygenation event [ 14 ]. Research has explored Rubisco evolution [ 15 – 19 ] and biochemistry [ 20 – 23 ], identifying several forms [ 24 – 26 ].…”

Section: Introductionmentioning

confidence: 99%

Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes

Asplund-Samuelsson

Hudson

2021

PLoS Comput Biol

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Knowledge of the genetic basis for autotrophic metabolism is valuable since it relates to both the emergence of life and to the metabolic engineering challenge of incorporating CO2 as a potential substrate for biorefining. The most common CO2 fixation pathway is the Calvin cycle, which utilizes Rubisco and phosphoribulokinase enzymes. We searched thousands of microbial genomes and found that 6.0% contained the Calvin cycle. We then contrasted the genomes of Calvin cycle-positive, non-cyanobacterial microbes and their closest relatives by enrichment analysis, ancestral character estimation, and random forest machine learning, to explore genetic adaptations associated with acquisition of the Calvin cycle. The Calvin cycle overlaps with the pentose phosphate pathway and glycolysis, and we could confirm positive associations with fructose-1,6-bisphosphatase, aldolase, and transketolase, constituting a conserved operon, as well as ribulose-phosphate 3-epimerase, ribose-5-phosphate isomerase, and phosphoglycerate kinase. Additionally, carbohydrate storage enzymes, carboxysome proteins (that raise CO2 concentration around Rubisco), and Rubisco activases CbbQ and CbbX accompanied the Calvin cycle. Photorespiration did not appear to be adapted specifically for the Calvin cycle in the non-cyanobacterial microbes under study. Our results suggest that chemoautotrophy in Calvin cycle-positive organisms was commonly enabled by hydrogenase, and less commonly ammonia monooxygenase (nitrification). The enrichment of specific DNA-binding domains indicated Calvin-cycle associated genetic regulation. Metabolic regulatory adaptations were illustrated by negative correlation to AraC and the enzyme arabinose-5-phosphate isomerase, which suggests a downregulation of the metabolite arabinose-5-phosphate, which may interfere with the Calvin cycle through enzyme inhibition and substrate competition. Certain domains of unknown function that were found to be important in the analysis may indicate yet unknown regulatory mechanisms in Calvin cycle-utilizing microbes. Our gene ranking provides targets for experiments seeking to improve CO2 fixation, or engineer novel CO2-fixing organisms.

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The Great Oxidation Event preceded a Paleoproterozoic “snowball Earth”

Cited by 116 publications

References 55 publications

dragon: A New Tool for Exploring Redox Evolution Preserved in the Mineral Record

dragon: A New Tool for Exploring Redox Evolution Preserved in the Mineral Record

Towards a new geological time scale: A template for improved rock-based subdivision of pre-Cryogenian time

Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes

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