Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

AbstractMethanogenic archaea are major contributors to the global carbon cycle and were long thought to belong exclusively to the euryarchaeotal phylum. Discovery of the methanogenesis gene cluster methyl-coenzyme M reductase (Mcr) in the Bathyarchaeota and thereafter the Verstraetearchaeota led to a paradigm shift, pushing back the evolutionary origin of methanogenesis to pre-date that of the Euryarchaeota. The methylotrophic methanogenesis found in the non-Euryarchaota distinguished itself from the predominantly hydrogenotrophic methanogens found in euryarchaeal orders as the former do not couple methanogenesis to carbon fixation through the reductive acetyl-coenzyme A (Wood-Ljungdahl) pathway, which was interpreted as evidence for independent evolution of the two methanogenesis pathways. Here, we report the discovery of a complete and divergent hydrogenotrophic methanogenesis pathway in a novel, thermophilic order of the Verstraetearchaeota which we have named Candidatus Methanohydrogenales, as well as the presence of the Wood-Ljungdahl pathway in the crenarchaeal order Desulfurococcales. Our findings support the ancient origin of hydrogenotrophic methanogenesis, suggest that methylotrophic methanogenesis might be a later adaptation of specific orders, and provide insight into how transition from hydrogenotrophic to methylotrophic methanogenesis might occur.

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Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1815631116 ◽

2019 ◽

Vol 116 (11) ◽

pp. 5037-5044 ◽

Cited By ~ 66

Author(s):

Bojk A. Berghuis ◽

Feiqiao Brian Yu ◽

Frederik Schulz ◽

Paul C. Blainey ◽

Tanja Woyke ◽

...

Keyword(s):

Paradigm Shift ◽

Carbon Fixation ◽

Methanogenic Archaea ◽

Global Carbon Cycle ◽

Hydrogenotrophic Methanogenesis ◽

Shared Ancestry ◽

Hydrogenotrophic Methanogens ◽

Methyl Coenzyme M Reductase ◽

Global Carbon ◽

Insight Into

Methanogenic archaea are major contributors to the global carbon cycle and were long thought to belong exclusively to the euryarchaeal phylum. Discovery of the methanogenesis gene cluster methyl-coenzyme M reductase (Mcr) in the Bathyarchaeota, and thereafter the Verstraetearchaeota, led to a paradigm shift, pushing back the evolutionary origin of methanogenesis to predate that of the Euryarchaeota. The methylotrophic methanogenesis found in the non-Euryarchaota distinguished itself from the predominantly hydrogenotrophic methanogens found in euryarchaeal orders as the former do not couple methanogenesis to carbon fixation through the reductive acetyl-CoA [Wood–Ljungdahl pathway (WLP)], which was interpreted as evidence for independent evolution of the two methanogenesis pathways. Here, we report the discovery of a complete and divergent hydrogenotrophic methanogenesis pathway in a thermophilic order of the Verstraetearchaeota, which we have named Candidatus Methanohydrogenales, as well as the presence of the WLP in the crenarchaeal order Desulfurococcales. Our findings support the ancient origin of hydrogenotrophic methanogenesis, suggest that methylotrophic methanogenesis might be a later adaptation of specific orders, and provide insight into how the transition from hydrogenotrophic to methylotrophic methanogenesis might have occurred.

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Reviews and syntheses: Heterotrophic fixation of inorganic carbon – significant but invisible flux in global carbon cycling

10.5194/bg-2020-465 ◽

2020 ◽

Author(s):

Alexander Braun ◽

Marina Spona-Friedl ◽

Maria Avramov ◽

Martin Elsner ◽

Federico Baltar ◽

...

Keyword(s):

Co2 Fixation ◽

Inorganic Carbon ◽

Carbon Fixation ◽

Standing Stock ◽

Co2 Flux ◽

Global Carbon Cycle ◽

Autotrophic Co2 Fixation ◽

Global Carbon ◽

Heterotrophic Biomass ◽

Heterotrophic Production

Abstract. Heterotrophic CO2 fixation is a significant, yet underappreciated CO2 flux in the global carbon cycle. In contrast to photosynthesis and chemolithoautotrophy – the main recognized autotrophic CO2 fixation pathways – the importance of heterotrophic CO2 fixation remains enigmatic. All heterotrophs – from microorganisms to humans – take up CO2 and incorporate it into their biomass. Depending on the available growth substrates, heterotrophic CO2 fixation contributes at least 2–8 % and in the case of methanotrophs up to 50 % of the carbon building up their biomass. Assuming a standing stock of global heterotrophic biomass of 47–85 Pg C, we estimate that up to 7 Pg C have been derived from heterotrophic CO2 fixation and up to 20 Pg C yr−1 originating from heterotrophic CO2 fixation are funneled into the global annual heterotrophic production of 34–245 Pg C yr−1. These first estimates on the importance of heterotrophic fixation of inorganic carbon indicate that this carbon fixation pathway should be included in present and future global carbon budgets.

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Deconstructing Methanosarcina acetivorans into an acetogenic archaeon

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2113853119 ◽

2022 ◽

Vol 119 (2) ◽

pp. e2113853119

Author(s):

Christian Schöne ◽

Anja Poehlein ◽

Nico Jehmlich ◽

Norman Adlung ◽

Rolf Daniel ◽

...

Keyword(s):

Carbon Monoxide ◽

Energy Conservation ◽

Carbon Fixation ◽

Coenzyme A ◽

Methanogenic Archaea ◽

Methanosarcina Acetivorans ◽

Acetyl Coa ◽

Acetyl Coenzyme A ◽

Acetyl Coenzyme ◽

Acetyl Coa Pathway

The reductive acetyl-coenzyme A (acetyl-CoA) pathway, whereby carbon dioxide is sequentially reduced to acetyl-CoA via coenzyme-bound C1 intermediates, is the only autotrophic pathway that can at the same time be the means for energy conservation. A conceptually similar metabolism and a key process in the global carbon cycle is methanogenesis, the biogenic formation of methane. All known methanogenic archaea depend on methanogenesis to sustain growth and use the reductive acetyl-CoA pathway for autotrophic carbon fixation. Here, we converted a methanogen into an acetogen and show that Methanosarcina acetivorans can dispense with methanogenesis for energy conservation completely. By targeted disruption of the methanogenic pathway, followed by adaptive evolution, a strain was created that sustained growth via carbon monoxide–dependent acetogenesis. A minute flux (less than 0.2% of the carbon monoxide consumed) through the methane-liberating reaction remained essential, indicating that currently living methanogens utilize metabolites of this reaction also for anabolic purposes. These results suggest that the metabolic flexibility of methanogenic archaea might be much greater than currently known. Also, our ability to deconstruct a methanogen into an acetogen by merely removing cellular functions provides experimental support for the notion that methanogenesis could have evolved from the reductive acetyl-coenzyme A pathway.

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Technical Note: Uncovering the influence of methodological variations on the extractability of iron bound organic carbon

10.5194/bg-2020-399 ◽

2020 ◽

Author(s):

Ben J. Fisher ◽

Johan C. Faust ◽

Oliver W. Moore ◽

Caroline L. Peacock ◽

Christian März

Keyword(s):

Organic Carbon ◽

Freeze Drying ◽

Global Carbon Cycle ◽

Technical Note ◽

Preparation Methods ◽

Reactive Iron ◽

Concentration Time ◽

Cbd Method ◽

Global Carbon ◽

Insight Into

Abstract. Association of organic carbon (OC) with reactive iron (FeR) represents an important mechanism by which OC is protected against remineralisation in soils and marine sediments. Recent studies indicate that the molecular structure of organic compounds and/or the identity of associated FeR phases exerts a control on the ability of an OC-FeR complex to be extracted by the citrate-bicarbonate-dithionite (CBD) method. While many variations of this method exist in the literature, these are often uncalibrated to each other, rendering comparisons of OC-FeR values extracted by different method iterations impossible. Here, we created a synthetic ferrihdyrite sample coprecipitated with simple organic structures and subjected these to modifications of the most common CBD method. Method parameters (reagent concentration, time of the extraction and sample preparation methods) were altered and FeR recovery measured to determine which (if any) modifications resulted in the greatest release of FeR from the sediment sample. We provide an assessment of the reducing capacity of Na dithionite in the CBD method and find that the concentration of dithionite deployed can limit OC-FeR extractability for sediments with a high FeR content. Additionally, we show that extending the length of any CBD extraction offers no benefit in removing FeR. Finally, we demonstrate that for synthetic OC-FeR samples, the almost universal technique of freeze drying samples can significantly reduce OC-FeR extractability and we offer insight into how this may translate to environmental samples using Arctic Ocean sediments. These results provide a valuable perspective on how the efficiency of this extraction could be improved to provide a more accurate assessment of sediment OC-FeR content. Accurate determinations of OC-FeR in sediments and soils represents an important step in improving our understanding of, and ability to model, the global carbon cycle.

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Energy Conservation and Hydrogenase Function in Methanogenic Archaea, in Particular the Genus Methanosarcina

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.00020-19 ◽

2019 ◽

Vol 83 (4) ◽

Cited By ~ 3

Author(s):

Thomas D. Mand ◽

William W. Metcalf

Keyword(s):

Energy Conservation ◽

Molecular Hydrogen ◽

Methanogenic Archaea ◽

Terminal Electron Acceptor ◽

Atp Production ◽

Formate Oxidation ◽

Wide Range ◽

Ion Gradient ◽

Global Carbon ◽

Insight Into

SUMMARY The biological production of methane is vital to the global carbon cycle and accounts for ca. 74% of total methane emissions. The organisms that facilitate this process, methanogenic archaea, belong to a large and phylogenetically diverse group that thrives in a wide range of anaerobic environments. Two main subgroups exist within methanogenic archaea: those with and those without cytochromes. Although a variety of metabolisms exist within this group, the reduction of growth substrates to methane using electrons from molecular hydrogen is, in a phylogenetic sense, the most widespread methanogenic pathway. Methanogens without cytochromes typically generate methane by the reduction of CO2 with electrons derived from H2, formate, or secondary alcohols, generating a transmembrane ion gradient for ATP production via an Na+-translocating methyltransferase (Mtr). These organisms also conserve energy with a novel flavin-based electron bifurcation mechanism, wherein the endergonic reduction of ferredoxin is facilitated by the exergonic reduction of a disulfide terminal electron acceptor coupled to either H2 or formate oxidation. Methanogens that utilize cytochromes have a broader substrate range, and can convert acetate and methylated compounds to methane, in addition to the ability to reduce CO2. Cytochrome-containing methanogens are able to supplement the ion motive force generated by Mtr with an H+-translocating electron transport system. In both groups, enzymes known as hydrogenases, which reversibly interconvert protons and electrons to molecular hydrogen, play a central role in the methanogenic process. This review discusses recent insight into methanogen metabolism and energy conservation mechanisms with a particular focus on the genus Methanosarcina.

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Phototrophic Methane Oxidation in a Member of the Chloroflexi Phylum

10.1101/531582 ◽

2019 ◽

Cited By ~ 6

Author(s):

Lewis M. Ward ◽

Patrick M. Shih ◽

James Hemp ◽

Takeshi Kakegawa ◽

Woodward W. Fischer ◽

...

Keyword(s):

Carbon Cycle ◽

Methane Oxidation ◽

Carbon Fixation ◽

Hot Spring ◽

Bacterial Genome ◽

Global Carbon Cycle ◽

Nitrite Reduction ◽

Biochemical Network ◽

Aerobic Respiration ◽

Global Carbon

AbstractBiological methane cycling plays an important role in Earth’s climate and the global carbon cycle, with biological methane oxidation (methanotrophy) modulating methane release from numerous environments including soils, sediments, and water columns. Methanotrophy is typically coupled to aerobic respiration or anaerobically via the reduction of sulfate, nitrate, or metal oxides, and while the possibility of coupling methane oxidation to phototrophy (photomethanotrophy) has been proposed, no organism has ever been described that is capable of this metabolism. Here we described a new bacterial genome from a member of the Chloroflexi phylum—termed hereCandidatusChlorolinea photomethanotrophicum—with cooccurring methanotrophy and phototrophy pathways, suggesting a novel link between these two metabolisms. Recovered as a metagenome-assembled genome from microbial mats in an iron-rich hot spring in Japan,Ca.‘C. photomethanotrophicum’ forms a new lineage within the Chloroflexi phylum and expands the known metabolic diversity of this already diverse clade.Ca.‘C. photomethanotrophicum’ appears to be metabolically versatile, capable of phototrophy (via a Type 2 reaction center), aerobic respiration, nitrite reduction, oxidation of methane and carbon monoxide, and potentially carbon fixation via a novel pathway composed of hybridized components of the serine cycle and the 3-hydroxypropionate bicycle. The biochemical network of this organism is constructed from components from multiple organisms and pathways, further demonstrating the modular nature of metabolic machinery and the ecological and evolutionary importance of horizontal gene transfer in the establishment of novel pathways.SignificanceMethane is a major greenhouse gas, and the production and consumption of methane is largely driven by the metabolism of microorganisms. Although it has been hypothesized for decades that some bacteria may be capable of growth by eating methane and conserving energy from sunlight (photomethanotrophy), this metabolism has never been discovered in nature. Here, we describe the first genetic evidence for a bacterium capable of photomethanotrophy, adding a new pathway to the known diversity of how microbes can make a living. This discovery also adds a new link to the global carbon cycle, and may provide new opportunities for designing biotechnological tools for processing methane.

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A repeat protein links Rubisco to form the eukaryotic carbon-concentrating organelle

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1522866113 ◽

2016 ◽

Vol 113 (21) ◽

pp. 5958-5963 ◽

Cited By ~ 90

Author(s):

Luke C. M. Mackinder ◽

Moritz T. Meyer ◽

Tabea Mettler-Altmann ◽

Vivian K. Chen ◽

Madeline C. Mitchell ◽

...

Keyword(s):

Carbon Fixation ◽

Low Complexity ◽

Global Carbon Cycle ◽

High Concentration ◽

Repeat Protein ◽

Photosynthetic Eukaryotes ◽

Lattice Arrangement ◽

Size Number ◽

Global Carbon

Biological carbon fixation is a key step in the global carbon cycle that regulates the atmosphere's composition while producing the food we eat and the fuels we burn. Approximately one-third of global carbon fixation occurs in an overlooked algal organelle called the pyrenoid. The pyrenoid contains the CO2-fixing enzyme Rubisco and enhances carbon fixation by supplying Rubisco with a high concentration of CO2. Since the discovery of the pyrenoid more that 130 y ago, the molecular structure and biogenesis of this ecologically fundamental organelle have remained enigmatic. Here we use the model green alga Chlamydomonas reinhardtii to discover that a low-complexity repeat protein, Essential Pyrenoid Component 1 (EPYC1), links Rubisco to form the pyrenoid. We find that EPYC1 is of comparable abundance to Rubisco and colocalizes with Rubisco throughout the pyrenoid. We show that EPYC1 is essential for normal pyrenoid size, number, morphology, Rubisco content, and efficient carbon fixation at low CO2. We explain the central role of EPYC1 in pyrenoid biogenesis by the finding that EPYC1 binds Rubisco to form the pyrenoid matrix. We propose two models in which EPYC1’s four repeats could produce the observed lattice arrangement of Rubisco in the Chlamydomonas pyrenoid. Our results suggest a surprisingly simple molecular mechanism for how Rubisco can be packaged to form the pyrenoid matrix, potentially explaining how Rubisco packaging into a pyrenoid could have evolved across a broad range of photosynthetic eukaryotes through convergent evolution. In addition, our findings represent a key step toward engineering a pyrenoid into crops to enhance their carbon fixation efficiency.

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