Methanosarcina

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Methanosarcina
Methanosarcina barkeri fusaro.gif
Methanosarcina barkeri fusaro
Scientific classification
Domain:
Archaea
Kingdom:
Euryarchaeota
Phylum:
Euryarchaeota
Class:
Methanomicrobia
Order:
Methanosarcinales
Family:
Methanosarcinaceae
Genus:
Methanosarcina

Kluyver and van Niel 1936
Type species
Methanosarcina barkeri
Schnellen 1947
Species
Synonyms
  • Sarcina ("Methanosarcina") (Kluyver & van Niel 1936) Breed 1948

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.

Contents

The amino acid pyrrolysine was first discovered in a Methanosarcina species, M. barkeri . Primitive versions of hemoglobin have been found in M. acetivorans, suggesting the microbe or an ancestor of it may have played a crucial role in the evolution of life on Earth. Species of Methanosarcina are also noted for unusually large genomes. M. acetivorans has the largest known genome of any archaeon.

According to a theory published in 2014, Methanosarcina may have been largely responsible for the largest extinction event in the Earth's history, the Permian–Triassic extinction event. The theory suggests that acquisition of a new metabolic pathway via gene transfer followed by exponential reproduction allowed the microbe to rapidly consume vast deposits of organic carbon in marine sediments, leading to a sharp buildup of methane and carbon dioxide in the Earth's oceans and atmosphere that killed around 90% of the world's species. This theory could better explain the observed carbon isotope level in period deposits than other theories such as volcanic activity.

Methanosarcina has been used in waste water treatment since the mid-1980s. Researchers have sought ways to use it as an alternative power source. Methanosarcina strains were grown in single-cell morphology (Sowers et al. 1993) at 35 °C in HS broth medium containing 125 mM methanol plus 40 mM sodium acetate (HS-MA medium).

Overview

Methanosarcina may be the only known anaerobic methanogens that produce methane using all three known metabolic pathways for methanogenesis. Methanogenesis is critical to the waste-treatment industry and biologically produced methane also represents an important alternative fuel source. Most methanogens make methane from carbon dioxide and hydrogen gas. Others utilize acetate in the acetoclastic pathway. In addition to these two pathways, species of Methanosarcina can also metabolize methylated one-carbon compounds through methylotrophic methanogenesis. Such one-carbon compounds include methylamines, methanol, and methyl thiols. [1] Only Methanosarcina species possess all three known pathways for methanogenesis, and are capable of utilizing no less than nine methanogenic substrates, including acetate.

Methanosarcina are the world's most diverse methanogens in terms of ecology. They are found in environments such as landfills, sewage heaps, deep sea vents, deep subsurface groundwater, and even in the gut of many different ungulates, including cows, sheep, goats, and deer. [1] Methanosarcina have also been found in the human digestive tract. [2] M. barkeri can withstand extreme temperature fluctuations and go without water for extended periods. It can consume a variety of compounds or survive solely on hydrogen and carbon dioxide. [3] It can also survive in low pH environments that are typically hazardous for life. [4] Noting its extreme versatility, biologist Kevin Sowers postulated that M. barkeri could even survive on Mars. [3] Methanosarcina grow in colonies and show primitive cellular differentiation. [1]

In 2002, the amino acid pyrrolysine was discovered in M. barkeri by Ohio State University researchers. [5] Earlier research by the team had shown that a gene in M. barkeri had an in-frame amber (UAG) codon that did not signal the end of a protein, as would normally be expected. This behavior suggested the possibility of an unknown amino acid which was confirmed over several years by slicing the protein into peptides and sequencing them. Pyrrolysine was the first genetically-encoded amino acid discovered since 1986, and 22nd overall. [6] It has subsequently been found throughout the family Methanosarcinaceae as well as in a single bacterium, Desulfitobacterium hafniense .

Both M. acetivorans and M. mazei have exceptionally large genomes. As of August 2008, M. acetivorans possessed the largest sequenced archaeal genome with 5,751,492 base pairs. The genome of M. mazei has 4,096,345 base pairs. [1]

Methanosarcina cell membranes are made of relatively short lipids, primarily of C25 hydrocarbons and C20 ethers. The majority of other methanogens have C30 hydrocarbons and a mixture of C20 and C40 ethers. [7] [8]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [9] and National Center for Biotechnology Information (NCBI). [10]

16S rRNA based LTP_06_2022 [11] [12] [13] 53 marker proteins based GTDB 08-RS214 [14] [15] [16]
Methanosarcina

M. balticavon Klein et al. 2002

M. semesiaeLyimo et al. 2000

M. lacustrisSimankova et al. 2002

M. subterraneaShimizu et al. 2015

M. siciliae(Stetter & K nig 1989) Ni et al. 1994

M. acetivoransSowers, Baron & Ferry 1986

M. horonobensisShimizu et al. 2011

M. mazeicorrig. (Barker 1936) Mah & Kuhn 1986

M. soligelidiWagner et al. 2013

M. barkeriSchnellen 1947

M. vacuolataZhilina & Zavarzin 1987

M. spelaeiGanzert et al. 2014

M. flavescensKern et al. 2016

M. thermophilaZinder et al. 1985

Methanosarcina

M. lacustris

M. horonobensis

M. mazei

M. acetivorans

M. siciliae

M. flavescens

M. thermophila

M. spelaei

M. barkeri

M. vacuolata

Role in early development of life on Earth

In 2004, two primitive versions of hemoglobin were discovered in M. acetivorans and another archaeon, Aeropyrum pernix . [17] Known as protoglobins, these globins bind with oxygen much as hemoglobin does. In M. acetivorans, this allows for the removal of unwanted oxygen which would otherwise be toxic to this anaerobic organism. Protoglobins thus may have created a path for the evolution of later lifeforms which are dependent on oxygen. [18] Following the Great Oxygenation Event, once there was free oxygen in Earth's atmosphere, the ability to process oxygen led to widespread radiation of life, and is one of the most fundamental stages in the evolution of Earth's lifeforms. [17]

Inspired by M. acetivorans, a team of Penn State researchers led by James G. Ferry and Christopher House proposed a new "thermodynamical theory of evolution" in 2006. It was observed that M. acetivorans converts carbon monoxide into acetate, the scientists hypothesized that early "proto-cells" attached to mineral could have similarly used primitive enzymes to generate energy while excreting acetate. The theory thus sought to unify the "heterotrophic" theory of early evolution, where the primordial soup of simple molecules arose from non-biological processes, and the "chemoautotrophic" theory, where the earliest lifeforms created most simple molecules. The authors observed that though the "debate between the heterotrophic and chemotrophic theories revolved around carbon fixation", in actuality "these pathways evolved first to make energy. Afterwards, they evolved to fix carbon." [2] The scientists further proposed mechanisms which would have allowed the mineral-bound proto-cell to become free-living and for the evolution of acetate metabolism into methane, using the same energy-based pathways. They speculated that M. acetivorans was one of the first lifeforms on Earth, a direct descendant of the early proto-cells. The research was published in Molecular Biology and Evolution in June 2006. [2]

Recently researchers have proposed an evolution hypothesis for acetate kinase and phosphoacetyl transferase with genomic evidence from Methanosarcina. [19] Scientists hypothesize acetate kinase could be the urokinase in a major protein superfamily that includes actin. [20] Evidence suggests acetate kinase evolved in an ancient halophilic Methanosarcina genome through duplication and divergence of the acetyl coA synthetase gene. [19]

Role in the Permian–Triassic extinction event

It was hypothesized that Methanosarcina's methane production may have been one of the causes of the Permian–Triassic extinction event. It is estimated that 70% of shell creatures died from ocean acidification, due to over-populated Methanosarcina. [21] A study conducted by Chinese and American researchers supports that hypothesis. Using genetic analysis of about 50 Methanosarcina genomes, the team concluded that the microbe likely acquired the ability to efficiently consume acetate using acetate kinase and phosphoacetyl transferase roughly 240 ± 41 million years ago, [lower-alpha 1] about the time of the extinction event 252 million years ago. [21] The genes for these enzymes may have been acquired from a cellulose-degrading bacterium via gene transfer. [22] Gene transfer plays an important role in the adaption of Methanosarcina species to their respective environment, with genomes of some species containing up to 31 % of genes acquired via gene transfer such as Methanosarcina mazei. [23]

The scientists concluded that these new genes, combined with widely available organic carbon deposits in the ocean and a plentiful supply of nickel, [lower-alpha 2] allowed Methanosarcina populations to increase dramatically. Under their theory, this led to the release of abundant methane as waste. [22] Then, some of the methane would have been broken down into carbon dioxide by other organisms. [24] The buildup of these two gases would have caused oxygen levels in the ocean to decrease dramatically, while also increasing acidity. Terrestrial climates would simultaneously have experienced rising temperatures and significant climate change from the release of these greenhouse gases into the atmosphere. It is possible the buildup of carbon dioxide and methane in the atmosphere eventually caused the release of hydrogen sulfide gas, further stressing terrestrial life. The team's findings were published in the Proceedings of the National Academy of Sciences in March 2014. [21]

The microbe theory's proponents argue that it would better explain the rapid, but continual, rise of carbon isotope level in period sediment deposits than volcanic eruption, which causes a spike in carbon levels followed by a slow decline. [22] The microbe theory suggests that volcanic activity played a different role - supplying the nickel which Methanosarcina required as a cofactor. Thus, the microbe theory holds that Siberian volcanic activity was a catalyst for, but not the primary cause of the mass extinction. [25]

Use by humans

In 1985, Shimizu Construction developed a bioreactor that uses Methanosarcina to treat waste water from food processing plants and paper mills. The water is fed into the reactor where the microbes break down the waste particulate. The methane produced by the archaea is then used to power the reactor, making it cheap to run. In tests, Methanosarcina reduced the waste concentration from 5,000–10,000 parts per million (ppm) to 80–100 ppm. Further treatment was necessary to finish the cleansing process. [26] According to a 1994 report in Chemistry and Industry, bioreactors utilizing anaerobic digestion by Methanothrix soehngenii or Methanosarcina produced less sludge byproduct than aerobic counterparts. Methanosarcina reactors operate at temperatures ranging from 35 to 55 °C and pH ranges of 6.5-7.5. [27]

Researchers have sought ways to utilize Methanosarcina's methane-producing abilities more broadly as an alternative power source. In December 2010, University of Arkansas researchers successfully spliced a gene into M. acetivorans that allowed it to break down esters. They argued that this would allow it to more efficiently convert biomass into methane gas for power production. [28] In 2011, it was shown that most methane produced during decomposition at landfills comes from M. barkeri. The researchers found that the microbe can survive in low pH environments and that it consumes acid, thereby raising the pH and allowing a wider range of life to flourish. They argued that their findings could help accelerate research into using archaea-generated methane as an alternate power source. [4]

Notes

  1. ↑ This value is the estimated date of the last common ancestor of those Methanosarcina strains able to grow readily on acetate.
  2. ↑ A nickel-tetrapyrrole coenzyme, cofactor F430, is present in methyl coenzyme M reductase, which catalyzes the final step in the release of methane by methanogens.

See also

Related Research Articles

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Marsh gas, also known as swamp gas or bog gas, is a mixture primarily of methane and smaller amounts of hydrogen sulfide, carbon dioxide, and trace phosphine that is produced naturally within some geographical marshes, swamps, and bogs.

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.

Methanotrophs 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.

Archaeoglobus is a genus of the phylum Euryarchaeota. Archaeoglobus can be found in high-temperature oil fields where they may contribute to oil field souring.

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.

Acidogenesis is the second stage in the four stages of anaerobic digestion:

Methanosarcina acetivorans is a versatile methane producing microbe which is found in such diverse environments as oil wells, trash dumps, deep-sea hydrothermal vents, and oxygen-depleted sediments beneath kelp beds. Only M. acetivorans and microbes in the genus Methanosarcina use all three known metabolic pathways for methanogenesis. Methanosarcinides, including M. acetivorans, are also the only archaea capable of forming multicellular colonies, and even show cellular differentiation. The genome of M. acetivorans is one of the largest archaeal genomes ever sequenced. Furthermore, one strain of M. acetivorans, M. a. C2A, has been identified to possess an F-type ATPase along with an A-type ATPase.

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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">Digestate</span> Material remaining after the anaerobic digestion of a biodegradable feedstock

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<span class="mw-page-title-main">Wood–Ljungdahl pathway</span> A set of biochemical reactions used by some bacteria

The Wood–Ljungdahl pathway is a set of biochemical reactions used by some bacteria. It is also known as the reductive acetyl-coenzyme A (acetyl-CoA) pathway. This pathway enables these organisms to use hydrogen as an electron donor, and carbon dioxide as an electron acceptor and as a building block for biosynthesis.

<span class="mw-page-title-main">Archaea</span> Domain of single-celled organisms

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Methanococcoides burtonii is a methylotrophic methanogenic archaeon first isolated from Ace Lake, Antarctica. Its type strain is DSM 6242.

Methanococcus maripaludis is a species of methanogenic archaea found in marine environments, predominantly salt marshes. M. maripaludis is a weakly motile, non-spore-forming, Gram-negative, strict anaerobic mesophile with a pleomorphic coccoid-rod shape, averaging 1.2 by 1.6 μm is size. The genome of M. maripaludis has been sequenced, and over 1,700 protein-coding genes have been identified. In ideal conditions, M. maripaludis grows quickly and can double every two hours.

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<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.

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References

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  14. ↑ "GTDB release 08-RS214". Genome Taxonomy Database . Retrieved 10 May 2023.
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