Methanotroph

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Methanotrophs (sometimes called methanophiles) are prokaryotes that metabolize methane as their source of carbon and chemical energy. They are bacteria or archaea, can grow aerobically or anaerobically, and require single-carbon compounds to survive.

Contents

Methanotrophs are especially common in or near environments where methane is produced, although some methanotrophs can oxidize atmospheric methane. Their habitats include wetlands, soils, marshes, rice paddies, landfills, aquatic systems (lakes, oceans, streams) and more. They are of special interest to researchers studying global warming, as they play a significant role in the global methane budget, by reducing the amount of methane emitted to the atmosphere. [1] [2]

Methanotrophy is a special case of methylotrophy, using single-carbon compounds that are more reduced than carbon dioxide. Some methylotrophs, however, can also make use of multi-carbon compounds; this differentiates them from methanotrophs, which are usually fastidious methane and methanol oxidizers. The only facultative methanotrophs isolated to date are members of the genus Methylocella silvestris , [3] [4] Methylocapsa aurea [5] and several Methylocystis strains. [6]

In functional terms, methanotrophs are referred to as methane-oxidizing bacteria. However, methane-oxidizing bacteria encompass other organisms that are not regarded as sole methanotrophs. For this reason, methane-oxidizing bacteria have been separated into subgroups: methane-assimilating bacteria (MAB) groups, the methanotrophs, and autotrophic ammonia-oxidizing bacteria (AAOB), which cooxidize methane. [2]

Classification

Methanotrophs can be either bacteria or archaea. Which methanotroph species is present is mainly determined by the availability of electron acceptors. Many types of methane oxidizing bacteria (MOB) are known. Differences in the method of formaldehyde fixation and membrane structure divide these bacterial methanotrophs into several groups. There are several subgroups among the methanotrophic archaea.

Methanotrophs have been historically classified broadly into three types which are defined by physiology, mechanism of methane metabolism, and morphology: Type I, II and X More recent literature has complicated these types by identifying overlapping characteristics in genetic makeup and the environmental conditions in which they are most likely to occur. [7] [8] [9] Generally, Type I methanotrophs tend to dominate in cold, anaerobic environments, meaning there is limited oxygen availability, which often have high methane concentrations. However, at a high enough salinity, Type II will dominate even in cold temperatures. [10] Type II methanotrophs tend to be more tolerant of stress and dominate in methane limited environments and acidic pHs. [11] As methanotroph research expands, there is less of a clear line between Type I and II methanotrophs, so familial or species classifications are more useful for grouping these organisms as seen in Table 1. [9] This table helps illuminate that methanotrophs that favor extreme environments, like hydrothermal vents, tend to uptake methane via the Calvin-Benson-Bassham Cycle (CBB). Research to understand why certain methanotrophs favor certain conditions and assimilation pathways is ongoing and relevant to predicting methanotroph responses to climate change.

Table 1: An updated classification of methanotrophs based on family. Displays the inability to distinguish between methanotrophs based upon methane oxidation pathway and environmental conditions alone. Taken from Fenibo et al., 2023. Methanotroph Classification.png
Table 1: An updated classification of methanotrophs based on family. Displays the inability to distinguish between methanotrophs based upon methane oxidation pathway and environmental conditions alone. Taken from Fenibo et al., 2023.

Aerobic

Under aerobic conditions, methanotrophs combine oxygen and methane to form formaldehyde, which is then incorporated into organic compounds via the serine pathway or the ribulose monophosphate (RuMP) pathway, and carbon dioxide, which is released. Type I and type X methanotrophs are part of the Gammaproteobacteria and they use the RuMP pathway to assimilate carbon. Type II methanotrophs are part of the Alphaproteobacteria and use the serine pathway of carbon assimilation. They also characteristically have a system of internal membranes within which methane oxidation occurs. Methanotrophs in Gammaproteobacteria are known from the family Methylococcaceae . [8] Methanotrophs from Alphaproteobacteria are found in families Methylocystaceae and Beijerinckiaceae .

Aerobic methanotrophs are also known from the Methylacidiphilaceae (phylum Verrucomicrobiota). [12] In contrast to Gammaproteobacteria and Alphaproteobacteria, methanotrophs in the phylum Verrucomicrobiota are mixotrophs. [13] [14] In 2021 a bacterial bin from the phylum Gemmatimonadota called "Candidatus Methylotropicum kingii" showing aerobic methanotrophy was discovered thus suggesting methanotrophy to be present in the four bacterial phyla. [15]

In some cases, aerobic methane oxidation can take place in anoxic environments. "Candidatus Methylomirabilis oxyfera" belongs to the phylum NC10 bacteria, and can catalyze nitrite reduction through an "intra-aerobic" pathway, in which internally produced oxygen is used to oxidise methane. [16] [17] In clear water lakes, methanotrophs can live in the anoxic water column, but receive oxygen from photosynthetic organisms, which they then directly consume to oxidize methane. [18]

No aerobic methanotrophic archaea are known.

Anaerobic

Under anoxic conditions, methanotrophs use different electron acceptors for methane oxidation. This can happen in anoxic habitats such as marine or lake sediments, oxygen minimum zones, anoxic water columns, rice paddies and soils. Some specific methanotrophs can reduce nitrate, [19] nitrite, [20] iron, [21] sulfate, [22] or manganese ions and couple that to methane oxidation without syntrophic partner. Investigations in marine environments revealed that methane can be oxidized anaerobically by consortia of methane oxidizing archaea and sulfate-reducing bacteria. [23] [24] This type of anaerobic oxidation of methane (AOM) mainly occurs in anoxic marine sediments. The exact mechanism is still a topic of debate but the most widely accepted theory is that the archaea use the reversed methanogenesis pathway to produce carbon dioxide and another, unknown intermediate, which is then used by the sulfate-reducing bacteria to gain energy from the reduction of sulfate to hydrogen sulfide and water.

The anaerobic methanotrophs are not related to the known aerobic methanotrophs; the closest cultured relatives to the anaerobic methanotrophs are the methanogens in the order Methanosarcinales. [25]

Special species

Methylococcus capsulatus is used to produce animal feed from natural gas. [26]

In 2010 a new bacterium Candidatus Methylomirabilis oxyfera from the phylum NC10 was identified that can couple the anaerobic oxidation of methane to nitrite reduction without the need for a syntrophic partner. [16] Based on studies of Ettwig et al., [16] it is believed that M. oxyfera oxidizes methane anaerobically by utilizing oxygen produced internally from the dismutation of nitric oxide into nitrogen and oxygen gas.

In addition to providing a natural methane sink, methanotrophs provide other services for humans. In wastewater treatment plants, the application of a mix of methanotrophic bacteria has the potential to reduce costs and increase overall efficiency at removing nitrogen and byproducts. [27] Depending upon environmental conditions, these methanotrophs can also produce biomolecules during the wastewater treatment process that are useful for a wide range of applications. [28] For example, methanotrophs undergoing glycolysis produce exopolysaccharides (EPS) which can be extracted and used in medicine. A well-known EPS is hyaluronic acid which is used widely in cosmetics and wound care.

Taxonomy

Many methanotrophic cultures have been isolated and formally characterized over the past 5 decades, starting with the classical study of Whittenbury (Whittenbury et al., 1970).  Currently, 18 genera of cultivated aerobic methanotrophic Gammaproteobacteria and 5 genera of Alphaproteobacteria are known, represented by approx. 60 different species. [29]

Methane oxidation

RuMP pathway.svg
RuMP pathway in type I methanotrophs
Serine pathway.svg
Serine pathway in type II methanotrophs

Methanotrophs oxidize methane by first initiating reduction of dioxygen to H2O2 and transformation of methane to CH3OH using methane monooxygenases (MMOs). [7] Furthermore, two types of MMO have been isolated from methanotrophs: soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO).

Cells containing pMMO have demonstrated higher growth capabilities and higher affinity for methane than sMMO containing cells. [7] It is suspected that copper ions may play a key role in both pMMO regulation and the enzyme catalysis, thus limiting pMMO cells to more copper-rich environments than sMMO producing cells. [30]

See also

Related Research Articles

<span class="mw-page-title-main">Nitrification</span> Biological oxidation of ammonia/ammonium to nitrate

Nitrification is the biological oxidation of ammonia to nitrate via the intermediary nitrite. Nitrification is an important step in the nitrogen cycle in soil. The process of complete nitrification may occur through separate organisms or entirely within one organism, as in comammox bacteria. The transformation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea.

Anaerobic respiration is respiration using electron acceptors other than molecular oxygen (O2). Although oxygen is not the final electron acceptor, the process still uses a respiratory electron transport chain.

Methanogenesis or biomethanation is the formation of methane coupled to energy conservation by microbes known as methanogens. It is the fourth and final stage of anaerobic digestion. Organisms capable of producing methane for energy conservation have been identified only from the domain Archaea, a group phylogenetically distinct from both eukaryotes and bacteria, although many live in close association with anaerobic bacteria. The production of methane is an important and widespread form of microbial metabolism. In anoxic environments, it is the final step in the decomposition of biomass. Methanogenesis is responsible for significant amounts of natural gas accumulations, the remainder being thermogenic.

<span class="mw-page-title-main">Anammox</span> Anaerobic ammonium oxidation, a microbial process of the nitrogen cycle

Anammox, an abbreviation for "anaerobic ammonium oxidation", is a globally important microbial process of the nitrogen cycle that takes place in many natural environments. The bacteria mediating this process were identified in 1999, and were a great surprise for the scientific community. In the anammox reaction, nitrite and ammonium ions are converted directly into diatomic nitrogen and water.

Methylotrophs are a diverse group of microorganisms that can use reduced one-carbon compounds, such as methanol or methane, as the carbon source for their growth; and multi-carbon compounds that contain no carbon-carbon bonds, such as dimethyl ether and dimethylamine. This group of microorganisms also includes those capable of assimilating reduced one-carbon compounds by way of carbon dioxide using the ribulose bisphosphate pathway. These organisms should not be confused with methanogens which on the contrary produce methane as a by-product from various one-carbon compounds such as carbon dioxide. Some methylotrophs can degrade the greenhouse gas methane, and in this case they are called methanotrophs. The abundance, purity, and low price of methanol compared to commonly used sugars make methylotrophs competent organisms for production of amino acids, vitamins, recombinant proteins, single-cell proteins, co-enzymes and cytochromes.

Denitrifying bacteria are a diverse group of bacteria that encompass many different phyla. This group of bacteria, together with denitrifying fungi and archaea, is capable of performing denitrification as part of the nitrogen cycle. Denitrification is performed by a variety of denitrifying bacteria that are widely distributed in soils and sediments and that use oxidized nitrogen compounds such as nitrate and nitrite in the absence of oxygen as a terminal electron acceptor. They metabolize nitrogenous compounds using various enzymes, including nitrate reductase (NAR), nitrite reductase (NIR), nitric oxide reductase (NOR) and nitrous oxide reductase (NOS), turning nitrogen oxides back to nitrogen gas or nitrous oxide.

<span class="mw-page-title-main">Methane monooxygenase</span> Class of enzymes

Methane monooxygenase (MMO) is an enzyme capable of oxidizing the C-H bond in methane as well as other alkanes. Methane monooxygenase belongs to the class of oxidoreductase enzymes.

Microbial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.

A chemocline is a type of cline, a layer of fluid with different properties, characterized by a strong, vertical chemistry gradient within a body of water. In bodies of water where chemoclines occur, the cline separates the upper and lower layers, resulting in different properties for those layers. The lower layer shows a change in the concentration of dissolved gases and solids compared to the upper layer.

Anaerobic oxidation of methane (AOM) is a methane-consuming microbial process occurring in anoxic marine and freshwater sediments. AOM is known to occur among mesophiles, but also in psychrophiles, thermophiles, halophiles, acidophiles, and alkophiles. During AOM, methane is oxidized with different terminal electron acceptors such as sulfate, nitrate, nitrite and metals, either alone or in syntrophy with a partner organism.

Methylocella silvestris is a bacterium from the genus Methylocella spp which are found in many acidic soils and wetlands. Historically, Methylocella silvestris was originally isolated from acidic forest soils in Germany, and it is described as Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped and methane-oxidizing facultative methanotroph. As an aerobic methanotrophic bacteria, Methylocella spp use methane (CH4), and methanol as their main carbon and energy source, as well as multi compounds acetate, pyruvate, succinate, malate, and ethanol. They were known to survive in the cold temperature from 4° to 30° degree of Celsius with the optimum at around 15° to 25 °C, but no more than 36 °C. They grow better in the pH scale between 4.5 to 7.0. It lacks intracytoplasmic membranes common to all methane-oxidizing bacteria except Methylocella, but contain a vesicular membrane system connected to the cytoplasmic membrane. BL2T (=DSM 15510T=NCIMB 13906T) is the type strain.

Methylosinus trichosporium is an obligate aerobic and methane-oxidizing bacterium species from the genus of Methylosinus. Its native habitat is generally in the soil, but the bacteria has been isolated from fresh water sediments and groundwater as well. Because of this bacterium's ability to oxidize methane, M. trichosporium has been popular for identifying both the structure and function of enzymes involved with methane oxidation since it was first isolated in 1970 by Roger Whittenbury and colleagues. Since its discovery, M. trichosporium and its soluble monooxygenase enzyme have been studied in detail to see if the bacterium could help in bioremediation treatments.

Methyloferula is a Gram-negative, mesophilic, psychrotolerant, aerobic and colorless genus of bacteria from the family of Beijerinckiaceae. Up to now there is only one species of this genus known.

<i>Methylacidiphilum fumariolicum</i> Species of bacterium

Methylacidiphilum fumariolicum is an autotrophic bacterium first described in 2007 growing on volcanic pools near Naples, Italy. It grows in mud at temperatures between 50 °C and 60 °C and an acidic pH of 2–5. It is able to oxidize methane gas. It uses ammonium, nitrate or atmospheric nitrogen as a nitrogen source and fixes carbon dioxide.

The sulfate-methane transition zone (SMTZ) is a zone in oceans, lakes, and rivers typically found below the sediment surface in which sulfate and methane coexist. The formation of a SMTZ is driven by the diffusion of sulfate down the sediment column and the diffusion of methane up the sediments. At the SMTZ, their diffusion profiles meet and sulfate and methane react with one another, which allows the SMTZ to harbor a unique microbial community whose main form of metabolism is anaerobic oxidation of methane (AOM). The presence of AOM marks the transition from dissimilatory sulfate reduction to methanogenesis as the main metabolism utilized by organisms.

An oxygen minimum zone (OMZ) is characterized as an oxygen-deficient layer in the world's oceans. Typically found between 200 m to 1500 m deep below regions of high productivity, such as the western coasts of continents. OMZs can be seasonal following the spring-summer upwelling season. Upwelling of nutrient-rich water leads to high productivity and labile organic matter, that is respired by heterotrophs as it sinks down the water column. High respiration rates deplete the oxygen in the water column to concentrations of 2 mg/L or less forming the OMZ. OMZs are expanding, with increasing ocean deoxygenation. Under these oxygen-starved conditions, energy is diverted from higher trophic levels to microbial communities that have evolved to use other biogeochemical species instead of oxygen, these species include nitrate, nitrite, sulphate etc. Several Bacteria and Archea have adapted to live in these environments by using these alternate chemical species and thrive. The most abundant phyla in OMZs are Pseudomonadota, Bacteroidota, Actinomycetota, and Planctomycetota.

<span class="mw-page-title-main">Hydrothermal vent microbial communities</span> Undersea unicellular organisms

The hydrothermal vent microbial community includes all unicellular organisms that live and reproduce in a chemically distinct area around hydrothermal vents. These include organisms in the microbial mat, free floating cells, or bacteria in an endosymbiotic relationship with animals. Chemolithoautotrophic bacteria derive nutrients and energy from the geological activity at Hydrothermal vents to fix carbon into organic forms. Viruses are also a part of the hydrothermal vent microbial community and their influence on the microbial ecology in these ecosystems is a burgeoning field of research.

<span class="mw-page-title-main">NC10 phylum</span> Phylum of bacteria

NC10 is a bacterial phylum with candidate status, meaning its members remain uncultured to date. The difficulty in producing lab cultures may be linked to low growth rates and other limiting growth factors.

<i>Methylomirabilis oxyfera</i> Bacteria species

Candidatus "Methylomirabilis oxyfera" is a candidate species of Gram-negative bacteria belonging to the NC10 phylum, characterized for its capacity to couple anaerobic methane oxidation with nitrite reduction in anoxic environments. To acquire oxygen for methane oxidation, M. oxyfera utilizes an intra-aerobic pathway through the reduction of nitrite (NO2) to dinitrogen (N2) and oxygen.

Methanoperedens nitroreducens is a candidate species of methanotrophic archaea that oxidizes methane by coupling to nitrate reduction.

References

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