Trace metal requirements for microbial enzymes involved in the production and consumption of methane and nitrous oxide

Abstract

Fluxes of greenhouse gases to the atmosphere are heavily influenced by microbiological activity. Microbial enzymes involved in the production and consumption of greenhouse gases often contain metal cofactors. While extensive research has examined the influence of Fe bioavailability on microbial CO(2) cycling, fewer studies have explored metal requirements for microbial production and consumption of the second- and third-most abundant greenhouse gases, methane (CH(4)), and nitrous oxide (N(2)O). Here we review the current state of biochemical, physiological, and environmental research on transition metal requirements for microbial CH(4) and N(2)O cycling. Methanogenic archaea require large amounts of Fe, Ni, and Co (and some Mo/W and Zn). Low bioavailability of Fe, Ni, and Co limits methanogenesis in pure and mixed cultures and environmental studies. Anaerobic methane oxidation by anaerobic methanotrophic archaea (ANME) likely occurs via reverse methanogenesis since ANME possess most of the enzymes in the methanogenic pathway. Aerobic CH(4) oxidation uses Cu or Fe for the first step depending on Cu availability, and additional Fe, Cu, and Mo for later steps. N(2)O production via classical anaerobic denitrification is primarily Fe-based, whereas aerobic pathways (nitrifier denitrification and archaeal ammonia oxidation) require Cu in addition to, or possibly in place of, Fe. Genes encoding the Cu-containing N(2)O reductase, the only known enzyme capable of microbial N(2)O conversion to N(2), have only been found in classical denitrifiers. Accumulation of N(2)O due to low Cu has been observed in pure cultures and a lake ecosystem, but not in marine systems. Future research is needed on metalloenzymes involved in the production of N(2)O by enrichment cultures of ammonia oxidizing archaea, biological mechanisms for scavenging scarce metals, and possible links between metal bioavailability and greenhouse gas fluxes in anaerobic environments where metals may be limiting due to sulfide-metal scavenging.

Keywords: enzymes; metals; methane; microbes; nitrous oxide.

Figure 1

Metal content of metalloenzymes in the three pathways of methanogenesis: H₂/CO₂ (black arrows), aceticlastic (green arrows), and methylotrophic (blue arrows). Each circle represents one metal atom. Parentheses show varying metal content of a given enzyme. Question marks mean that enzyme may not be present in all methanogens (6×[Fe₄S₄] and 10×[Fe₄S₄]polyferredoxins are encoded in the eha operon and a 14×[Fe₄S₄]polyferredoxin is encoded in the ehb operon). Abbreviations: CA, carbonic anhydrase; Cdh, carbon monoxide dehydrogenase/acetyl-CoA synthase; Ech/Eha/Ehb/Mbh, energy-converting hydrogenase; Fd, ferredoxin; Fmd/Fwd, Mo/W formylmethanofuran dehydrogenase; Frh, F₄₂₀-reducing hydrogenase; Hdr, heterodisulfide reductase; Hmd, Ni-free Fe hydrogenase; Mcr, methyl coenzyme M reductase; Mta, methanol-coenzyme M methyltransferase; Mtr, CH₃-H₄M(S)PT-coenzyme M methyltransferase; Vh(o/t)/Mvh, Ni–Fe hydrogenase. For simplicity, only metalloenzymes are labeled. See the Section “Metalloenzymes in Methanogenesis” for more details, abbreviations for intermediates and enzyme substitutions that occur in specific conditions and species.

Figure 2

Metal content of the enzymes involved in aerobic methanotrophy at high or low Cu, and intra-aerobic methane oxidation coupled with denitrification. Each circle represents one metal atom. Abbreviations: Cyt, cytochrome; DL-FalDH, dye-linked formaldehyde dehydrogenase; FDH, formate dehydrogenase; MDH, methanol dehydrogenase; pMMO, Cu-particulate methane monooxygenase; sMMO, soluble methane monooxygenase; NirS, Fe–nitrite reductase; NOD, NO dismutase (putative enzyme). Putative intra-aerobic methane oxidation coupled with denitrification pathway is adapted from Wu et al. (2011). For simplicity, only metalloenzymes are labeled. Question marks mean that the metal content of the enzyme is not well known, and for the case of NOD, that the enzyme is unknown. See the Section “Metalloenzymes in Aerobic Methanotrophy” for more details.

Figure 3

Metal content of three pathways of N₂O production: classical denitrification, bacterial nitrifier denitrification, and archaeal ammonia oxidation. Each circle represents one metal atom. Parentheses show varying metal content of a given enzyme. Abbreviations: AMO, ammonia monooxygenase; HAO, hydroxylamine oxidoreductase; Nar, dissimilatory nitrate reductase; NirS, Fe–nitrite reductase; NirS, Cu–nitrite reductase; cNOR, nitric oxide reductase; Nos, nitrous oxide reductase; NXOR, nitroxyl oxidoreductase (putative enzyme). Putative archaeal ammonia oxidation pathway is adapted from Walker et al. (2010). For simplicity, only metalloenzymes are labeled. Question marks depict unknown or unconfirmed enzymes. Enzymes colored a solid purple indicate that an unknown amount of Cu is present. See the Section “Metalloenzymes Involved in the Production and Consumption of Nitrous Oxide” for more details.