NO connection with methane

Microorganisms that grow by oxidizing methane come in two basic types, aerobic and anaerobic. Now we have something in between that generates its own supply of molecular oxygen by metabolizing nitric oxide.

On page 543 of this issue, Ettwig et al.1 report their discovery of a new type of methane-oxidizing (methanotrophic) bacterium, provisionally dubbed Methylomirabilis oxyfera. As its name suggests, this microbe does something quite unexpected: the process involved could provide another angle on our understanding of the biology and chemistry of the early Earth, and perhaps even extend to the possibility of life on other methane-rich bodies in the Solar System.

Methylomirabilis oxyfera conducts what seems to be an anaerobic, nitrite-linked oxidation of methane (CH4) via a denitrification pathway to yield nitrogen and carbon dioxide. But Ettwig et al. show that this organism defies convention and, by means of a putative nitric oxide (NO) dismutase enzyme, reacts to produce N2 and oxygen. The intracellular O2 produced is used to metabolize methane via the well-described pathway of aerobic methanotrophy initiated by the enzyme methane monooxygenase (Fig. 1a). NO dismutase is one of just a handful of enzymes that are known to evolve molecular oxygen. Hence, M. oxyfera can consume methane in anoxic environments that are rich in nitrogen oxides, such as the freshwater sloughs contaminated with nitrogenous fertilizer run-off investigated by Ettwig and colleagues. Nevertheless, the bacterium is at heart a cryptic aerobe, but rather than getting its O2 from the atmosphere, it generates its own from the ambient nitrite. Essentially, it contains its own little scuba tank that allows it to 'breathe' oxygen while immersed in methane-rich anoxic muck, thereby accessing the methane that conventional methanotrophs cannot reach.

Figure 1: Four modes of methane metabolism by microorganisms.

a, Nitrite-linked methane (CH4) oxidation by Methylomirabilis oxyfera1. Nitrate (NO3) is reduced to nitrite (NO2) by other microbes; M. oxyfera reduces the nitrite to nitric oxide (NO), after which it undergoes a dismutative reaction to yield N2 and O2. This intracellular oxygen is the ultimate oxidant for a conventional 'aerobic' pathway of methane oxidation (c) initiated by particulate methane monooxygenase. b, Methanogenesis by anaerobic processing of organic matter, yielding fermentation products, and then H2 and CO2, which serve as substrates for consumption by methanogenic archaea. c, Aerobic oxidation of methane, as displayed by bacteria such as Methylococcus capsulatus that can exploit the interfaces between methane-rich anoxic environments and oxygen-rich aerobic environments to obtain supplies of both gases. d, Reverse methanogenesis: anaerobic oxidation of methane (AOM) involving an archaeon (designated ANME) related to the methanogens. The ANME microbe oxidizes the methane in a sequence opposite to that of methane formation in b. An unknown intermediate [?] is exchanged between the ANME and sulphate-reducing bacteria (SRB). The sulphate-reducers act in a relationship that ultimately allows the carbon in methane to be oxidized to CO2, and the electrons generated by that reaction reduce sulphate (SO42−) to hydrogen sulphide (H2S).

Methane is nature's simplest hydrocarbon. It first endeared itself to me when I was an undergraduate slogging through my first semester of organic chemistry. One simple carbon atom surrounded by four hydrogen atoms: ah, but an entire course could be structured around this deceptively simple molecule and its relevance to such topics as basic microbiology, planetary evolution, geochemistry, petroleum geology, energy economics, global warming and even astrobiology.

The basic fact here is that methane burns well and has economic value. It is the prime component of natural gas, and is also renewable through the degradation of fermentable organic molecules in concert with microbes referred to as methanogenic archaea (Fig. 1b). Moreover, it exists as enormous deposits on the sea floor in solid form as a clathrate2, in principle offering a way to solve our energy problems. But here lies the rub. After water vapour and CO2, methane is the most important greenhouse gas in Earth's troposphere (the lowest 10 kilometres or so of the atmosphere). If massive release of methane comes from the breakdown of seabed clathrates, as may have occurred in the distant past3, there would be a rapid and highly disruptive pattern of global change.

Enter the methanotrophs, which make a living by consuming methane, either by interception on its upward transit from sites of biological production or geological storage, or by uptake from the troposphere. By oxidizing methane to CO2 they reduce its outward flux to the atmosphere and, along with reaction with hydroxyl radicals, help to regulate methane abundance in the troposphere4.

There are two known routes by which methane can be oxidized and support the growth of microorganisms: aerobic and anaerobic. The aerobic pathway has been well studied and is characterized by Methylococcus capsulatus, which oxidizes methane with molecular oxygen, forming CO2, water and biomass (Fig. 1c). These bacteria are isolated by classic means, and their cellular workings have been unravelled by standard biochemistry, now greatly aided by the progress made in DNA sequencing and genetics, and with computer databases.

Anaerobic oxidation of methane is a more complicated story. It was first postulated by marine geochemists, who observed vertical profiles of methane abundance in anoxic marine systems that suggested in situ biological consumption, with sulphate acting as the ultimate oxidant, or terminal electron acceptor. This is analogous to how O2 works in the aerobic pathway, but sulphate is a much weaker oxidant than O2 and hence the reaction does not yield much energy for bacterial growth. The fact that these microbes could not be cultivated made microbiologists (myself included) discount the phenomenon. But technological advances have changed the game: recalcitrant microbes need not be cultivated to support astonishing findings. Thus, it emerged that a specialized group of anaerobic microorganisms, closely related to the methanogenic archaea ('ANMEs'), conduct the reverse reaction and make a living by oxidizing methane back to CO2, with sulphate-reducing bacteria acting in a mutually beneficial relationship5 (Fig. 1d).

Ettwig and colleagues' studies1 involved detailed metagenomic analyses and biochemical assays of cultures that were highly enriched in M. oxyfera, and with their discovery we have something that lies in the grey area between aerobic and anaerobic methane oxidation (Fig. 1a). The broader question is what importance a process such as that mediated by M. oxyfera has beyond the confines of anoxic agricultural streams. Is it a biological adaptation responding to environmental niches created by human-induced pollution? Is it something more significant with respect to Earth's history, harking back to the times before the great oxidation event (about 2.45 billion years ago), when our planet's atmosphere was devoid of oxygen and was presumably methane-rich? Or maybe it was a means to harness the abundant methane of Earth's middle years, when a still-limited oxygen tension allowed for the oxidation of ammonium and the accumulation of 'suboxic' anions such as nitrite to serve as electron acceptors.

Such concepts go beyond the realm of Earth, and can be extrapolated to Mars (where methane is present as an atmospheric trace gas) or even Titan (where it occurs as liquid precipitation and shallow lakes). Do alien, anaerobic microbes exist somewhere on these orbs to take advantage of the abundant supply of carbon and energy that methane supplies?


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Oremland, R. NO connection with methane. Nature 464, 500–501 (2010).

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