Natural and anthropogenic processes generate carbon monoxide (CO). They are responsible for a CO emission of 2500–2600 teragram (Tg) per year. Most CO is emitted by natural processes including atmospheric CH4 oxidation, natural hydrocarbon oxidation, volcanic activity, production by plants and photochemical degradation of organic matter in water, soil, and marine sediments or from the enzymatic degradation of heme. Anthropogenic processes such as incomplete combustion of fossil fuels and various industrial processes are responsible for an annual release of 1200 Tg of CO to the atmosphere. Carboxydotrophic microorganisms Kroneck et al. , 2014 Chemical and biological processes are responsible for CO removal. The major part of CO in the atmosphere becomes oxidized to CO2 by rapid reaction with hydroxyl radicals in the troposphere (2000–2800 Tg/yr), reducing the half-life of CO in the troposphere to a few months. Biological processes are relevant to remove CO and keep it at low trace gas concentrations. Microbes consume CO by using it as a source of carbon and energy. Soil and marine microbes reduce the global budget of CO by 20% per year, to which soil microbes contribute with 200–600 Tg of CO removal per year. CO-oxidizing bacteria have a natural enrichment in the top layer of burning charcoal piles from where several of these soil microbes have been isolated. CO is also consumed by pathogenic Mycobacteria, like the tubercle bacillus Mycobacterium tuberculosis, which can grow on CO as sole source of carbon and energy. Carboxydotrophic microorganisms Kroneck et al. , 2014 Reaction equations and their standard Gibbs free energy (G0) for several modes of carboxydotrophic growth Diender et al. , 2015 Isolated microorganisms capable of conserving energy from the water–gas shift reaction Carboxydotrophic microorganisms Diender et al. , 2015 Carboxydotrophic microorganisms Isolated microorganisms capable of conserving energy from the water–gas shift reaction Kroneck et al. , 2014 Carboxydotrophic microorganisms Carboxydotrophic microorganisms Kroneck et al. , 2014 Cu,Mo-containing CO dehydrogenases Kroneck et al. , 2014 Monofunctional Ni,Fe-containing CO dehydrogenases Kroneck et al. , 2014 Monofunctional Ni,Fe-containing CO dehydrogenases Kroneck et al. , 2014 Bifunctional Ni,Fe-containing CO dehydrogenases Kroneck et al. , 2014 Rittmann et al. , 2015 Carboxydotrophic microorganisms Rittmann et al. , 2015 Carboxydotrophic microorganisms Carboxydotrophic microorganisms Diender et al. , 2015 Diender et al. , 2015 Carboxydotrophic microorganisms Methanogenesis Dr. Simon K.-M. R. Rittmann Methanogens Methanothermobacter marburgensis DSM 2133, phase contrast micrograph (magnification x 1000) © Simon K.-M. R. Rittmann Nomura et al., 2007, Advanced Powder Technology Wagner et al., 2007, IJSEM M. barkeriM. marburgensis M. solegelidi 10µm The cell wall is composed of pseudomurein. Cell wall of Sarcina is composed of a S-layer lattice, but under special environmental conditions Sarcina also form a methanochondoitin layer encapsulating an association of cells enabling intercellular e- transfer. are obligate anaerobic prokaryotes from the domain Archaea, exclusively belong to the phylum Euryarchaeota (and possibly Bathyarchaeota, Lokiarchaeota); produce methane as end product of their energy metabolism; use carbon substrates such as C1-, C2- and methylated compounds Six classes of methanogens Sorokin et al., 2018 Eight orders of methanogens 1. Methanobacterales 2. Methanocellales 3. Methanococcales 4. Methanomassiliicoccales 5. Methanomicrobiales 6. Methanonatronarchaeles 7. Methanopyrales 8. Methanosarcinales Borrel et al.,2013, Iino et al., 2013, Sorokin et al., 2018 Methanogenesis – Global carbon cycle Thauer et al. 2008 Thauer et al. (2010) Ann. Rev. Biochem. Methanogenesis – Global carbon cycle Sources of GHG emissions Tian et al., 2016TD… top down, BU… bottom up Sources of CH4 emissions Liu and Whitman, 2008 Nazaries et al., 2013 Ruminants, agriculture and fossil fuel exploitation are large anthropogenic sources of methane emissions Rumen and reticulum are hydrolysis and fermentation chambers, anaerobic, 100-150 L, 200-250 liters CH4 d-1 (~ 3.4 mmol L-1 h-1). Ruminants and methane (Speiseröhre) (Labmagen) (Blättermagen) (Netzmagen)(Pansen) Poulsen et al., 2012 Ruminants and methane TMA, Methanomassiliicoccales and health Origin and fate of TMA in the human gut, and the Archaebiotics concept. Gut microbiota synthesis of TMA is realized from TMAO , choline, PC and Lcarnitine. The TMA is then absorbed and goes to the liver, routes (A) or (B). In the case of route (A), a partial or total defect in a flavin- containing monooxygenase 3 (FMO 3)-oxidation into TMAO leads to increased level and diffusion of TMA in breath, urine and sweat. When FMO 3 (liver oxidation) is functional (B), the increase of TMAO in blood is associated with atherosclerosis.2,7,11 Therefore, converting TMA directly in the gut using Archaebiotics belonging to the seventh methanogenic order, naturally-occurring in the gut, route (C) should be envisaged. Interestingly, these archaea are only able to perform methanogenesis using methyl compounds (see Fig. 2), because the two other pathways are absent (CO2 reduction with H2 and aceticlastic pathway): this would increase the efficiency of TMA conversion. Brugère et al., 2014 Methane from coal Welte 2016 Methane from coal Mayumi et al., 2016 Methoxydotrophic methanogenesis from various MACs. (A) Methanogenesis from seven types of MACs by 10 type strains and one isolate belonging to the order Methanosarcinales. Each MAC was supplied with methoxy groups to a final concentration of 30 mM. Methane produced was measured after incubation for 9 months. Data are means of three individual incubations; error bars represent SD of these triplicates. (B) Substrate ranges of Methermicoccus shengliensis strains AmaM and ZC-1 for 40 types of MACs; an asterisk designates MACs analyzed for the media with coal samples. For each substrate, the average amount of methane produced (n = 3) is expressed by one of four ranges. Detailed methane production data are shown in table S1. Mayumi et al., 2016 Mayumi et al., 2016 Methane from coal Methane from coal Mayumi et al., 2016 Methane from coal Mayumi et al., 2016 Methanogenesis – Thawing permafrost Mondav et al. (2014) Nature Communications Mondav et al., 2014 Methanogenesis – Thawing permafrost Taubner et al., 2015 Methanogenesis – psychrophilic strains Taubner et al., 2015A plot of specific growth rates (µ) of four methanogenic strains Methanogenesis – growth rate Purwatini et al., 2014 Methanogenesis – 4 pathways Methanogenesis – 4 pathways CO2-type pathway Methyl-group type pathways Thauer et al., 2008; Borrel et al., 2013 Core reactions Aceticlastic pathway Thermodynamically, two reactions are exergonic and, hence, involved in energy conservation: 1)The methyl transfer from H4MPT to CoM by methyl-tetrahydromethanopterin:CoM methyltransferase (Mtr) 2)The reduction of the CoM-S-S-CoB heterodisulfide by heterodisulfide reductase (Hdr) Methanogenesis – Gibbs free energy Liu &Whitman 2008 Diender et al. , 2015 Carboxydotrophic methanogens Methanogenic archaea capable of metabolizing CO Diender et al. , 2015 Carboxydotrophic methanogens Ferry, 2010 Carboxydotrophic methanogens Ferry, 2010 Carboxydotrophic methanogens Ferry, 2010 Pathway for conversion of CO to acetate and methane by the marine isolate Methanosarcina acetivorans. Fd Ferredoxin, THSPt tetrahydrosarcinapterin, HS-CoB coenzyme B, HS CoM coenzyme M, MF methanofuran Carboxydotrophic methanogens Methanogens with & without cytochromes Thauer et al., 2008 Methanogens with cytochromes Thauer et al., 2008 Ferry, 2010 Acetoclastic methanogens Methanogens with cytochromes Welte & Deppenmeier, 2014 Methanogens with cytochromes Welte & Deppenmeier, 2014 Methanogens with cytochromes Welte & Deppenmeier, 2014 Methanogens with cytochromes Welte & Deppenmeier, 2014 Methanogens with cytochromes Welte & Deppenmeier, 2014 Methanogens with cytochromes Welte & Deppenmeier, 2014 Methanogens with cytochromes Welte & Deppenmeier, 2014 Methanogens with cytochromes Welte & Deppenmeier, 2014 Thauer et al. 2010 H2 uptake in methanogenic archaea Thauer et al. 2010 H2 uptake in methanogenic archaea H2 uptake in methanogenic archaea Thauer et al. 2010 The structures and functions of (b) the VhtACG complex. The Vht complex is found only in methanogens with cytochromes. H2 uptake in methanogenic archaea Thauer et al. 2010 The structures and functions of (c) the FrhABG complex. H2 uptake in methanogenic archaea Thauer et al. 2010 The proposed function and localization within the cell of the [NiFe]-hydrogenases involved in methanogenesis from H2 and CO2 are shown for methanogens (a) with cytochromes and (b) without cytochromes Thauer et al. 2010 H2 uptake in methanogenic archaea Methanogens without cytochromes Thauer et al., 2008 Methanogens without cytochromes Thauer et al., 2008 The structures and functions of (a) the MvhADG/HdrABC complex. The Mvh/Hdr complex is found mainly in methanogens without cytochromes, The stoichiometry of the MvhADG/HdrABCcatalyzed reaction has not yet been ascertained. H2 uptake in methanogenic archaea Thauer et al., 2008, 2010 Methanogens – e- bifurcation Purwatini et al., 2014 Methanogens – e- bifurcation Lie et al. 2012 Costa et al., 2013(c) Methanogens – e- bifurcation Thauer 2012 Methanogens without cytochromes Methanogens without cytochromes Thauer et al., 2008 Metabolism of methanogens – Ca. M. termitum Lang et al., 2015 Metabolism of methanogens – Ca. M. termitum Metabolism of methanogens – Ca. M. termitum Lang et al., 2015 Evans et al. 2015 Candidatus phylum Barthyarchaeota Evans et al. (2015) Science Candidatus phylum Barthyarchaeota Candidatus phylum Barthyarchaeota Evans et al., 2015 Candidatus phylum Verstraetearchaeota Vanvonterghem et al., 2016 Proposed metabolism of the Verstraetearchaeota. a, Pathways for methylotrophic methanogenesis, hydrogen cycling and suggested energy conservation mechanisms. The first mechanism is shown in blue and entails heterodisulfide reduction by HdrABC–MvhABDG coupled to ferredoxin reoxidation by an Fpo-like (dark blue) or Ehb (light blue) complex. The second mechanism involves HdrD coupled directly to the Fpo-like complex (light green), and the third possibility links HdrD to an FAD hydrogenase (dark green). b, Other metabolic pathways including potential sugar and amino acid utilization, an incomplete TCA cycle and a nucleotide salvage pathway. Black arrows indicate genes that were found in all near-complete Verstraetearchaeota genomes (V1–V4), and grey arrows represent genes that are present in only a subset of the genomes (coloured circles indicate in which subset of genomes they are found). Dashed light grey arrows show parts of a pathway that are missing in all genomes.Vanvonterghem et al., 2016 Candidatus phylum Verstraetearchaeota WSA2 (a) catabolism and (b) anabolism. (a) WSA2 has genes for H2 oxidation through electron-bifurcating hydrogenase (HdrABC–MvhDGA) and H2 cycling by energy-converting hydrogenase (EhbA-Q); CO oxidation by carbon monoxide dehydrogenase (CODH); and methylated thiol reduction and methanogenesis by methylated thiol Coenzyme M methyltransferase corrinoid fusion protein (MtsA) and methyl coenzyme M reductase (McrABG). The proton motive force (or cation gradient) generated by Ehb can support ATP production by ATP synthase. (b) Malonate decarboxylase and acetyl-CoA synthetase can convert malonate and acetate into acetyl-CoA for downstream co-assimilation with CO2 (bolded) through pyruvate:ferredoxin oxidoreductase, pyruvate carboxylase and tricarboxylic acid (TCA) cycle. As identified for other heterotrophic methanogens, WSA2 does not encode the glyoxylate shunt for acetate assimilation (gray with dotted line). The methylmalonyl-CoA pathway can facilitate co-assimilation of propionate and CO2 also into the TCA cycle. WSA2 can use key TCA cycle intermediates (pink) as building blocks for biosynthesis. Candidatus Methanofastidiosa Candidatus Methanofastidiosum methylthiophilus Nobu et al., 2016 Candidatus phylum Methanofastidiosa Coenzymes and cofactors participating in reactions common to all methanogenic pathways. Methanosarcina species synthesize tetrahydrosarcinapterin (H4SPT), which serves the same function as tetrahydromethanopterin (H4MPT) and has a similar structure except for a terminal α-linked glutamate (113). Ferry et al. 2010 Methanogenesis – cofactors Ferry et al. 2010 Methanogenesis – cofactors Methyl-coenzyme M reductase Shima & Thauer, 2005 a2b2g2 Ermler et al., 1997 mcrA/mrtA isoenzymes are used as molecular marker for detection of methanogens! Methyl-coenzyme M reductase Wongnate et al., 2016 Methyl-coenzyme M reductase Wongnate et al., 2016 Initial steps in three mechanisms of MCR catalysis. Mechanism I involves nucleophilic attack of Ni(I)-MCRred1 on the methyl group of methyl-SCoM to generate a methylNi(III) intermediate (34). This mechanism is similar to that of B12-dependent methyltransferases (48), which generate a methyl-cob(III) alamin intermediate. In mechanism II, Ni(I) attack on the sulfur atom of methyl-SCoM promotes the homolytic cleavage of the methyl-sulfur bond to produce a methyl radical (•CH3) and a Ni(II)-thiolate. Mechanism III involves nucleophilic attack of Ni(I) on the sulfur of methyl-SCoM to form a highly reactive methyl anion and Ni(III)-SCoM (MCRox1). Methyl-coenzyme M reductase Proposed steps of mechanism II. In the first step, Ni(I) attack on the sulfur of methylSCoM leads to homolytic cleavage of the C-S bond and generation of a methyl radical and a Ni(II)-thiolate (MCRox1-silent). Next, Hatom abstraction from CoBSH generates methane and the CoBS• radical, which in the third step combines with the Nibound thiolate of CoM to generate the Ni(II)-disulfide anion radical. Then, oneelectron transfer to Ni(II) generates MCRred1 and the heterodisulfide (CoBSSCoM) product, which dissociates leading to ordered binding of methyl-SCoM and CoBSH and initiation of the next catalytic cycle. Wongnate et al., 2016