Methanobacterium

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Methanobacterium
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Methanobacterium formicicum
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Archaea
Kingdom: Euryarchaeota
Class: Methanobacteria
Order: Methanobacteriales
Family: Methanobacteriaceae
Genus: Methanobacterium
Kluyver and van Niel 1936
Type species
Methanobacterium formicicum
Schnellen 1947
Species

See text

Synonyms
  • "Bacterium" ("Methanobacterium") (Kluyver & van Niel 1936) Breed et al. 1948

Methanobacterium is a genus of the Methanobacteria class in the Archaea kingdom, which produce methane as a metabolic byproduct. [1] Despite the name, this genus belongs not to the bacterial domain but the archaeal domain (for instance, they lack peptidoglycan in their cell walls). [2] Methanobacterium are nonmotile and live without oxygen, [2] which is toxic to them, and they only inhabit anoxic environments. [3]

A shared trait by all methanogens is their ability to recycle products. [3] They can use the products of metabolic activities occurring during methanogenesis as substrates for the formation of methane. [3] Methanobacterium species typically thrive in environments with optimal growth temperatures ranging from 28 to 40 °C, and in versatile ecological ranges. [4] They are a part of the scientific world that is still relatively unknown, but methanogens are thought to be some of earth’s earliest life forms. [4] They do not create endospores when nutrients are limited. [2] They are ubiquitous in some hot, low-oxygen environments, such as anaerobic digesters, wastewater, and hot springs. [5]

Discovery

In 1776, Alesandro Volta discovered that gas bubbles coming from a freshwater swamp were flammable. [6] This finding lead him to believe that methane gas could be produced by living organisms, however, he thought that this methane was coming from decomposing organic matter. [6] In 1993, methanogens were first cultured, revealing that this methane was coming from living organisms. [6]

Diversity and taxonomy

Methanobacterium are a specific genus within the methanogen species. The evolutionary history of Methanobacterium is still relatively unknown, but methanogens are thought to be some of earth’s earliest life forms, with origins dating back over 3.4 billion years. [4]

Methanogens, including Methanobacterium species, belong to the archaea domain, characterized by unique features such as unconventional 16S rRNA sequences, distinct lipid structures, and novel cell wall compositions. [7] These organisms are prevalent in extreme environments but are also found in more moderate habitats, exhibiting a wide range of growth temperatures from psychrotrophic to hyperthermophilic, and varying salinity preferences from freshwater to saturated brine. [7] Despite their taxonomic placement within archaea, methanogens display diverse cellular envelopes, which can consist of protein surface layers (S-layers), glycosylated S-layer proteins, additional polymers like methanochondroitin, or pseudomurein in Gram-positive staining species. [7] Methanogens are unique among archaea in their adaptability to a broad spectrum of environmental conditions, with a preference for neutral to moderately alkaline pH values. [7]

Taxonomically, methanogens are classified into 25 genera, distributed across 12 families and five orders, highlighting the substantial phenotypic and genotypic diversity within this group. [7] This taxonomic diversity suggests that methanogenesis, the metabolic pathway through which methanogens produce methane, is an ancient and widespread trait. [7] The monophyletic nature of modern methanogens indicates that methanogenesis likely evolved only once, with all contemporary methanogens sharing a common ancestor. [7] Recent taxonomic schemes reflect the rich diversity and evolutionary history of methanogens, underscoring their importance in anaerobic microbial ecosystems and their intriguing adaptation to diverse environmental niches. [7]

Each species of Methanobacterium is capable of the syntropic process of methane production, with a majority of the species being hydrogenotrophic. [3] The species differ in their ability to use different substrates for the methane production process. The substrates utilized in the methane production process can be hydrogenotrophic, methylotrophic, or acetoclastic. [3]

Species

There are many different species of Methanobacterium with officially recognized names. [8] A few and listed and described below:

Methanobacterium formicicum is an archaeon found in the rumen of cattle, buffalo, sheep, goats and other animals. [9] Microbes in the gut, degrade nutrients from feed (polysaccharides, proteins, and fats) into organic molecules which later are turned into methane by Methanobacterium such as Methanobacterium formicicum. [9] Methanobacterium formicicum can be found in the human gut as well as in animals and can cause gastrointestinal and metabolic disorders in both humans and animals. [9]

Methanobacterium oryzae was isolated from rice field soil in the Philippines. [10] Methanobacterium, such as Methanobacterium oryzae, that thrive in rice fields often use hydrogen and acetate as their main energy source. [10] This Methanobacterium as well as other species of Methanobacterium found in rice field soils from around the world are a major source of methane which is a dominant greenhouse gas. [10]

Methanobacterium palustre thrives in marshland areas and was first found in a peat bog. [11]

Methanobacterium arcticum was isolated from permafrost sediments in the Russian Arctic. [8] This species of Methanobacterium uses only hydrogen, carbon dioxide, and formate as fuel. [8] Unlike some other Methanobacteria, it does not use acetate to grow. [8]

Methanobacterium thermoautotrophicum Marburg can undergo natural genetic transformation, the transfer of DNA from one cell to another. [12] Genetic transformation in archaeal species, generally, appears to be an adaptation for repairing DNA damage in a cell by utilizing intact DNA information derived from another cell. [13]

Methanobacterium thermaggregans were found from fed-batch fermentation. [14] M. thermaggregans is alkophilic and thermophilic. [14] This was based on the findings of M. thermaggregans being able to alter an increase of agitated speeds that is used to increase methane formulation. [14]

Genome

The genome of seven different Methanobacterium and Methanobrevibacter have been sequenced. [9] Methanobacterium has a strain that demonstrates a genome of approximately 1,350 sequences. [15] About 190 of those strains are specific in BRM9 genes, which are correlated to proteins or prophage. [15] It includes mesophilic methanogens from various anaerobic conditions. [15] However, they carry a tiny amount of methanogen characteristic within the rumen. [15] These genes, which are used for their central metabolism and their pseudomurein cell wall, propose that the species is capable of inhibition by the small molecule inhibitor and vaccine. [15] This is determined by the methane alleviation devices that have the ability to grow the genes found in the rumen. [15]

Methanobacterium plays a role in both the waste and water waste processes due to its abilities of degrading organic substances. [16] Methanobacterium are normally isolated from natural oxygen deficient environments such as, freshwater, marine sediments, wet soils, the rumen and the intestines of animals, humans, and insects. [16] Through molecular findings of the 16S rRNA and mcrA gene, which encodes the methyl coenzyme M reductase on the alpha subunit, shows that there are additional unidentified methanogens that exist in other ecosystems. [16]

Morphology

Methanobacterium are generally bacillus-shaped microbes. [2] Because there are many different species in the Methanobacterium genus, there are a variety of shapes, sizes, and arrangements these microbes can possess. [17] These rod shaped microbes can be curved, straight, or crooked. [2] They can also range in size, can be short or long, and can be found individually, in pairs, or in chains. [17] Some Methanobacterium species can even be found in large clusters or aggregates which consist of long intertwined chains of individual microbes. [18]

There have been many strains of Methanobacterium that have been isolated and studied profoundly. One particular strain of Methanobacterium that has been isolated and studied is Methanobacteriumthermoautotrophicum. [19] This revealed the presence of intracytoplasmic membranes, an internal membrane system consisting of 3 membranes stacked on top of each other without a cytoplasm separating them. [19] Methanobacterium palustre is another strain that further confirms a large characteristic of Methanobacterium is a gram-positive cell wall, lacking a peptidoglycan layer outside of its cytoplasmic membrane. [20] The cell wall of the family Methanobacteriaea consists of pseudomurein, [21] a carbohydrate backbone and a cross-linking peptide with amino acids that form the peptide bonds and serve the nature of the bonding and sugar type. [22]

Physiology

Methanobacterium are strict anaerobes, meaning they cannot survive in the presence of oxygen. [2] Most species belonging to this genus are also autotrophs which create organic compounds from inorganic materials such as carbon dioxide. [23] Methanobacterium can be classified as hydrogenotrophic methanogens. [23] Hydrogenotrophic methanogens use hydrogen, carbon dioxide, formate, and alcohols to synthesize methane. [23] These substrates are also important for the growth and maintenance of Methanobacterium. [23] Methanogenesis is a vital part of the carbon cycle as it performs the conversion of organic carbon into methane gas. [7]

This part of the carbon cycle is referred to as the methanogenesis cycle. It is a process involving three different kinds of carbon dioxide reduction, which ultimately lead to the production of methane. [7] However, within each separate pathway, there are intermediary products that are used as substrates in some other part of the cycle. The interconnectedness of products and substrates are defined by the term syntropic. [7] The cycling substrates can be arranged into 3 groups based on the whether the autotrophic carbon dioxide (CO2) reduction was with hydrogen gas (H2), formate (CH2O2), or secondary alcohols. [3] Some members of this genus can use formate to reduce methane; others live exclusively through the reduction of carbon dioxide with hydrogen. [7]

Optimal growth temperature

Methanobacterium species typically thrive in environments with optimal growth temperatures ranging from 28 to 40°C. [4] Methanobacteria are widely distributed in geothermal settings like hot springs and hydrothermal vents. [4] This mesophilic temperature range indicates that Methanobacterium organisms are adapted to moderate environmental conditions, neither extremely hot nor cold. [24] This temperature preference allows them to inhabit a variety of anaerobic environments, including soil, sediments, and animal digestive tracts, where conditions often fall within this mesophilic range. [4] Within these habitats, Methanobacterium species contribute to methane production through their hydrogenotrophic metabolism, utilizing hydrogen and carbon dioxide as metabolic substrates. [4]

Habitat

Methanobacterium species inhabit various anaerobic environments, showcasing a versatile ecological range. [2] They can be found in diverse habitats such as soil, wetlands, sediment layers, sewage treatment plants, and the gastrointestinal tracts of animals. [4] Within these environments, Methanobacterium species play crucial roles in anaerobic microbial ecosystems, contributing to processes like organic matter decomposition via methane production through the methanogenesis pathway. [4]

In the human gut

Methanobacterium is found in the human colon. [25] It is involved in managing the amount of calories that is being consumed, by influencing the process of bacterial breakdown. [25]

There are two specific groups that have undergone isolation and culture from the human intestines. [26] However, methanogens have also been discovered in colostrum and breast milk from mothers who are healthy and lactating. [26] This was discovered from performing the techniques of quantitative polymerase chain reaction (qPCR), culture, and amplicon sequencing. [26]

A species of Methanobacterium called M. smithii is found in the human intestines. [26] M. smithii is able to  integrate glycans within the intestines for fixing, which is used for regulating protein expression. [26] An increase of methane concentration in human residue is correlated with BMI. [26]

Methanogens remove hydrogen that remains in the gut, based on hydrogen accumulation in the intestines that can reduce the productivity of the microbial activities. [26] Methanogens can also be used as probiotics. [26] This is possible since methanogens are capable of using trimethylamine as a substrate for methanogenesis. [26] Trimethylamine is produced in the human intestines by intestinal bacteria. [26] An increase of trimethylamine may cause cardiovascular disease. [26] These methanogens are able to utilize hydrogen to decrease trimethylamine while it is growing in the intestines. [26]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature [27] and the National Center for Biotechnology Information. [28]

16S rRNA based LTP_08_2023 [29] [30] [31] 53 marker proteins based GTDB 08-RS214 [32] [33] [34]
Methanobacterium

M. flexileZhu, Liu & Dong 2011

M. alkalithermotoleransMei et al. 2022

M. alcaliphilum Worakit et al. 1986

M. movensZhu, Liu & Dong 2011

M. aarhusense Shlimon et al. 2004

M. beijingense Ma, Liu & Dong 2005

M. movilensecorrig. Schirmack et al. 2014

M. oryzae Joulian et al. 2000

M. bryantii Balch & Wolfe 1981

M. ivanovii Jain et al. 1988

M. veterum Krivushin et al. 2010

M. arcticum Shcherbakova et al. 2011

M. espanolae Patel, Sprott & Fein 1990

species‑group 2
Methanobacterium

M. lacusBorrel et al. 2012

M. paludisCadillo-Quiroz et al. 2014

M. aggregansKern, Linge & Rother 2015

M. congolense Cuzin et al. 2001

M. formicicum Schnellen 1947

M. palustre Zellner et al. 1990

M. subterraneum Kotelnikova, Macario & Pedersen 1998

M. ferruginis Mori & Harayama 2011

M. kanagienseKitamura et al. 2011

M. petrolearium Mori & Harayama 2011

Methanobacterium
species‑group 2
Methanobacterium

Methanosphaera

Unassigned species:

See also

Related Research Articles

Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They belong to the domain Archaea and are members of the phylum Euryarchaeota. Methanogens are common in wetlands, where they are responsible for marsh gas, and can occur in the digestive tracts of animals including ruminants and humans, where they are responsible for the methane content of belching and flatulence. In marine sediments, the biological production of methane, termed methanogenesis, is generally confined to where sulfates are depleted below the top layers. Methanogens play an indispensable role in anaerobic wastewater treatments. Other methanogens are extremophiles, found in environments such as hot springs and submarine hydrothermal vents as well as in the "solid" rock of Earth's crust, kilometers below the surface in the deep biosphere.

Methanogenesis or biomethanation is the formation of methane coupled to energy conservation by microbes known as methanogens. 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.

An acetogen is a microorganism that generates acetate (CH3COO−) as an end product of anaerobic respiration or fermentation. However, this term is usually employed in a narrower sense only to those bacteria and archaea that perform anaerobic respiration and carbon fixation simultaneously through the reductive acetyl coenzyme A (acetyl-CoA) pathway (also known as the Wood-Ljungdahl pathway). These genuine acetogens are also known as "homoacetogens" and they can produce acetyl-CoA (and from that, in most cases, acetate as the end product) from two molecules of carbon dioxide (CO2) and four molecules of molecular hydrogen (H2). This process is known as acetogenesis, and is different from acetate fermentation, although both occur in the absence of molecular oxygen (O2) and produce acetate. Although previously thought that only bacteria are acetogens, some archaea can be considered to be acetogens.

<i>Methanosarcina</i> Genus of archaea

Methanosarcina is a genus of euryarchaeote archaea that produce methane. These single-celled organisms are known as anaerobic methanogens that produce methane using all three metabolic pathways for methanogenesis. They live in diverse environments where they can remain safe from the effects of oxygen, whether on the earth's surface, in groundwater, in deep sea vents, and in animal digestive tracts. Methanosarcina grow in colonies.

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.

In biology, syntrophy, syntrophism, or cross-feeding is the cooperative interaction between at least two microbial species to degrade a single substrate. This type of biological interaction typically involves the transfer of one or more metabolic intermediates between two or more metabolically diverse microbial species living in close proximity to each other. Thus, syntrophy can be considered an obligatory interdependency and a mutualistic metabolism between different microbial species, wherein the growth of one partner depends on the nutrients, growth factors, or substrates provided by the other(s).

<span class="mw-page-title-main">Methanobacteria</span> Class of archaea

Methanobacteria is a class of archaeans in the kingdom Euryarchaeota. Several of the classes of the Euryarchaeota are methanogens and the Methanobacteria are one of these classes.

Methanobacteriales is an order of archaeans in the class Methanobacteria. Species within this order differ from other methanogens in that they can use fewer catabolic substrates and have distinct morphological characteristics, lipid compositions, and RNA sequences. Their cell walls are composed of pseudomurein. Most species are Gram-positive with rod-shaped bodies and some can form long filaments. Most of them use formate to reduce carbon dioxide, but those of the genus Methanosphaera use hydrogen to reduce methanol to methane.

<i>Methanothermobacter</i> Genus of archaea

Methanothermobacter is a genus of archaeans in the family Methanobacteriaceae. The species within this genus are thermophilic and grow best at temperatures between 55 °C and 65 °C. They are methanogens; they use carbon dioxide and hydrogen as substrates to produce methane for energy.

<span class="mw-page-title-main">Coenzyme-B sulfoethylthiotransferase</span> Class of enzymes

In enzymology, coenzyme-B sulfoethylthiotransferase, also known as methyl-coenzyme M reductase (MCR) or most systematically as 2-(methylthio)ethanesulfonate:N-(7-thioheptanoyl)-3-O-phosphothreonine S-(2-sulfoethyl)thiotransferase is an enzyme that catalyzes the final step in the formation of methane. It does so by combining the hydrogen donor coenzyme B and the methyl donor coenzyme M. Via this enzyme, most of the natural gas on earth was produced. Ruminants produce methane because their rumens contain methanogenic prokaryotes (Archaea) that encode and express the set of genes of this enzymatic complex.

<span class="mw-page-title-main">Cofactor F430</span> Chemical compound

F430 is the cofactor (sometimes called the coenzyme) of the enzyme methyl coenzyme M reductase (MCR). MCR catalyzes the reaction EC 2.8.4.1 that releases methane in the final step of methanogenesis:

<i>Methanococcus maripaludis</i> Species of archaeon

Methanococcus maripaludis is a species of methanogenic archaea found in marine environments, predominantly salt marshes. M. maripaludis is a non-pathogenic, gram-negative, weakly motile, non-spore-forming, and strictly anaerobic mesophile. It is classified as a chemolithoautotroph. This archaeon has a pleomorphic coccoid-rod shape of 1.2 by 1.6 μm, in average size, and has many unique metabolic processes that aid in survival. M. maripaludis also has a sequenced genome consisting of around 1.7 Mbp with over 1,700 identified protein-coding genes. In ideal conditions, M. maripaludis grows quickly and can double every two hours.

<i>Methanosarcina barkeri</i> Species of archaeon

Methanosarcina barkeri is the most fundamental species of the genus Methanosarcina, and their properties apply generally to the genus Methanosarcina. Methanosarcina barkeri can produce methane anaerobically through different metabolic pathways. M. barkeri can subsume a variety of molecules for ATP production, including methanol, acetate, methylamines, and different forms of hydrogen and carbon dioxide. Although it is a slow developer and is sensitive to change in environmental conditions, M. barkeri is able to grow in a variety of different substrates, adding to its appeal for genetic analysis. Additionally, M. barkeri is the first organism in which the amino acid pyrrolysine was found. Furthermore, two strains of M. barkeri, M. b. Fusaro and M. b. MS have been identified to possess an F-type ATPase along with an A-type ATPase.

Methanobrevibacter oralis is a methanogenic archaeon species considered to be a member of the human microbiota, mainly associated to the oral cavity. M. oralis is a coccobacillary shaped, single-cell, Gram-positive, non-motile microorganism of the Archaea domain of life. This species has been isolated and sequenced from humans in dental plaque and in their gastrointestinal tract. As a methanogen and a hydrogenotroph, this prokaryote can produce methane by using hydrogen and carbon dioxide as substrates through a process called methanogenesis.

Hydrogenotrophs are organisms that are able to metabolize molecular hydrogen as a source of energy.

Methanogens are a group of microorganisms that produce methane as a byproduct of their metabolism. They play an important role in the digestive system of ruminants. The digestive tract of ruminants contains four major parts: rumen, reticulum, omasum and abomasum. The food with saliva first passes to the rumen for breaking into smaller particles and then moves to the reticulum, where the food is broken into further smaller particles. Any indigestible particles are sent back to the rumen for rechewing. The majority of anaerobic microbes assisting the cellulose breakdown occupy the rumen and initiate the fermentation process. The animal absorbs the fatty acids, vitamins and nutrient content on passing the partially digested food from the rumen to the omasum. This decreases the pH level and initiates the release of enzymes for further breakdown of the food which later passes to the abomasum to absorb remaining nutrients before excretion. This process takes about 9–12 hours.

Biological methanation (also: biological hydrogen methanation (BHM) or microbiological methanation) is a conversion process to generate methane by means of highly specialized microorganisms (Archaea) within a technical system. This process can be applied in a power-to-gas system to produce biomethane and is appreciated as an important storage technology for variable renewable energy in the context of energy transition. This technology was successfully implemented at a first power-to-gas plant of that kind in the year 2015.

In enzymology, a formylmethanofuran dehydrogenase (EC 1.2.99.5) is an enzyme that catalyzes the chemical reaction:

Ralph Stoner Wolfe was an American microbiologist, who contributed to the discovery of the single-celled archaea as the third domain of life. He was a pioneer in the biochemistry of methanogenesis.

<span class="mw-page-title-main">Hydroxyarchaeol</span> Chemical compound

Hydroxyarchaeol is a core lipid unique to archaea, similar to archaeol, with a hydroxide functional group at the carbon-3 position of one of its ether side chains. It is found exclusively in certain taxa of methanogenic archaea, and is a common biomarker for methanogenesis and methane-oxidation. Isotopic analysis of hydroxyarchaeol can be informative about the environment and substrates for methanogenesis.

References

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  31. ↑ "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
  32. ↑ "GTDB release 08-RS214". Genome Taxonomy Database . Retrieved 10 May 2023.
  33. ↑ "ar53_r214.sp_label". Genome Taxonomy Database . Retrieved 10 May 2023.
  34. ↑ "Taxon History". Genome Taxonomy Database . Retrieved 10 May 2023.
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