Methanosarcina

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Methanosarcina
Methanosarcina barkeri, strain Fusaro

Methanosarcina barkeri , strain Fusaro

Systematics
Domain : Archaea (Archaea)
Department : Euryarchaeota
Class : Methanomicrobia
Order : Methanosarcinales
Family : Methanosarcinaceae
Genre : Methanosarcina
Scientific name
Methanosarcina
Kluyver & van Niel 1936

Methanosarcina is a genus of prokaryotic microorganisms . Methanosarcina belongs to the domain of the living organisms Archaea , is anaerobic and forms methane .

Summary of properties

Boone & Mah (2015) summarize the properties of the genus Methanosarcina as follows:

Irregular spheroidal bodies (1–3 µm in diameter ) that appear alone or typically in cell aggregates ( aggregates up to 1000 µm in diameter). Sometimes they appear as large cysts with individual coccoid cells and a common outer wall. Endospores are not formed. The results of Gram staining are variable. Not movable. Cells can Gas - vesicles contain. Strictly anaerobic . The optimal growth temperatures are 30–40 ° C for mesophilic species and 50–55 ° C for thermophilic species. Energy metabolism through the formation of methane from acetate , methanol , monomethylamine , dimethylamine , trimethylamine , H 2 / CO 2 and CO . Some tribes do not use H 2 / CO 2 as the only energy substrate. Very slow growth with pyruvate can occur. N 2 fixation can occur. The G + C content of the DNA is 36–43 % .

Cell shape and cell boundary

One of the first mentions with the Dutch name "Methaansarcine" in 1906 already indicates the most obvious properties of the later genus: The name Methanosarcina means something like "methane-forming package" and was derived from a neo-Latin word for methane ("the methanum ") and the Latin word for package or bundle ("the Sarcina "). In a fundamental work on the classification of methane-producing microorganisms from 1979, it was determined with regard to the morphology that the members of the family Methanosarcinaceae (and thus also of the genus Methanosarcina ) are irregular, gram-positive cocci that would form packets of different sizes. These lumps would be large enough to be seen with the naked eye. The planes of division of the cells in the package would not necessarily be vertical. It should be noted that the result of a Gram stain strongly depends on the cell wall structure that occurs in each case; In 2015, this result was not classified as gram-positive, but as variable.

The development of the morphology of different species and strains depends heavily on the preferred salt concentration and the salt concentration actually present in the growth environment. M. barkeri, for example, shows a dichotomous morphology : when these microbes are grown in freshwater medium, they grow into large, multicellular aggregates that are embedded in a matrix of so-called methanochondroitin, while in an environment similar to seawater they appear as individual, irregular cocci that are only surrounded by a protein layer ( S-layer ), but not by methanochondroitin.

Methanochondroitin is a heterogeneous polysaccharide and in some respects resembles chondroitin in connective tissue of vertebrates . The Methanosarcina - cell membranes are made of relatively short lipids constructed primarily of C25 hydrocarbons and C20 ethers enter, while the cell membranes of most other Methanbildner C30 hydrocarbons and a mixture of C20 and C40 include ethers (C20, C25, etc., the Number of carbon atoms in the respective molecular chain).

Methanosarcina cells do not form spores .

Metabolism and Genetics

Methanosarcina is an anaerobic species, although for M. acetivorans that is actually an obligatory anaerobes has shown is that this archaeon microaerophilic withstand conditions. In M. acetivorans and another archaeon, Aeropyrum pernix , heme- binding globins were discovered that could bind oxygen as well as hemoglobin and in which Freitas et al. Saw previous versions of hemoglobin, which is why they called them protoglobins. The authors saw the most likely function of these proteins in the detoxification of oxygen. The first heme protein with a known function in archaea is a sensor that mediates aerotaxis in Halobacterium salinarum ( Hs -HemAT). The escape from oxygen by aerotaxis is ruled out for Methanosarcina, however, since the archaeon is considered immobile. The investigations of a heme-binding protein (MA4561) in M. acetivorans indicated a heme- based sensor, which reflects the redox potential of its environment and influences the gene regulation of the methyl sulfide metabolism and therefore, according to the authors, MsmS (methyl sulfide methyltransferase-associated sensor) should be called.

Methanosarcina is possibly the only known methanogen that can produce methane via all known metabolic pathways of methanogenesis . Most methane formers make methane from the gases carbon dioxide and hydrogen and others use acetate in the acetic acid-splitting way (the so-called acetoclastic way). In addition to these two pathways, types of methanosarcine can produce methane from organic substances that contain exactly one carbon atom (C1 or one-carbon compounds) (methylotrophic methanogenesis). Such C1 compounds include methylamines , methanol, and methylthiols . Methanosarcina species can produce methane from at least nine substrates .

Some types of Methanosarcina can also use carbon monoxide (CO) for methanogenesis. In M. barkeri four CO molecules by a CO dehydrogenase (CODH) to be carbon dioxide (CO 2 oxidized) and then, the reduction of CO 2 to methane, with hydrogen (H 2 ) as the electron donor is used. Therefore, growth with H 2 and CO 2 is also possible. In contrast, the CO metabolism of M. acetivorans is different. M. acetivorans cells can also use CO, but not with H 2 and CO 2 , since there is no corresponding hydrogenase system . In addition, the organism produces large amounts of acetate and formate from CO during methanogenesis .

In 2002, the pyrrolysine in M. barkeri was published as the 22nd proteinogenic amino acid . Previous research had shown that there is a gene in M. barkeri that has a codon that would normally signal the end (stop codon UAG ) of a protein , but does not. This behavior suggested that an unusual amino acid might be incorporated into the protein, similar to that of the 21st proteinogenic amino acid, selenocysteine . Studies have been carried out over several years which confirmed the incorporation of pyrrolysine into a protein (press release). The amino acid pyrrolysine was subsequently found in the entire Methanosarcinaceae family as well as in the bacterium Desulfitobacterium hafniense .

Some species of Methanosarcina have relatively large genomes . With 5,751,492 base pairs , M. acetivorans had the largest sequenced archaea genome to date in August 2008, and a range of 4,096,345 base pairs was given for the genome of M. mazei .

The comparison of genomes between phylogenetically closely and distantly related species revealed peculiarities of Methanosarcina , e.g. B. for the acetate kinase gene and other genes that play a role in the activation of acetate in the metabolism (comments on acetate kinase and activation). Methanosarcina species are the only archaea found so far that have an acetate kinase, while this enzyme is common in bacteria . This suggests that the gene in question was transferred by horizontal gene transfer.

The search for the origin of metabolic pathways and for the developmental steps forms the background of the considerations on acetate kinase. In 2001 the assumption was published that acetate kinase is the "primal kinase" in a large protein superfamily . This protein superfamily is based on members who ATPase - domains have and includes such diverse proteins such. B. Kinases for cell cycle functions, heat shock proteins and actin .

There are various assumptions about the origin of acetate kinase (and about the origin of other genes or proteins associated with the topic, e.g. phosphoacetyltransferase and acetyl-CoA synthetase) that have in common that methanosarcina should be included in the considerations. Fournier & Gogarten (2008), for example, favored the transfer of a cellulose- degrading bacterium to a Methanosarcina ancestor and Barnhard et al. (2015) were more likely to assume that the acetate kinase in Methanosarcina on a duplicated based gene that previously for a subunit of acetyl-CoA - synthetase (ADP-Acs-α) encodes had.

Systematics

The taxonomic information on the genus Methanosarcina comes from the LPSN (List of Prokaryotic names with Standing in Nomenclature), accessed 2019-04. The direct parent taxon of the genus Methanosarcina is the family Methanosarcinaceae. The genus Methanosarcina has 16 species at the time of retrieval ; the type species is M. barkeri .

Historical summary of the naming and classification :

A basis for the description of the genus was laid in 1906 and the genus Methanosarcina was described in 1936 with the first species Methanosarcina methanica . The names " Methanosarcina Kluyver & van Niel 1936 " for the genus and " Methanosarcina methanica (Smit 1930) Kluyver & van Niel 1936 " for the type species were confirmed in 1980. Due to a publicationfrom 1979 to classify methanogens, Methanosarcina was determined as a type genus of the new family "Methanosarcinaceae Balch & Wolfe 1981 ".

" Methanosarcina barkeri Schnellen 1947 " has been the new type species of Methanosarcina since 1986 , as no suitable strain could be found to describe M. methanica . With regard to the type strain of Methanosarcina barkeri , there was a debate which was ultimately decided (1987) in favor of the strain DSM 800 T (MS T ).

ecology

Occurrence

Methanosarcina species are ecologically the most diverse methane producers worldwide . They exist in all sorts of anaerobic environments such as landfills, sewage heaps, deep sea springs, deep groundwater, and even in the intestines of many different ungulates including cattle, sheep, goats, and deer.

Methanosarcina cells do not form spores , but at least one species ( M. barkeri ) can dry out and endure unfavorable conditions in this state, e.g. B. high temperature fluctuations. They can also survive in low pH environments that are usually life threatening. It has been suggested that M. barkeri could briefly survive on Mars (press release).

Syntrophies

The methane-forming archaea often live in syntrophic microbe communities with bacteria that are also anaerobic . Since Methanosarcina has a wide range of methanogenesis possibilities, it is not surprising that the way in which the syntrophies are used is also characterized by diversity. Such relationships of Methanosarcina barkeri in defined mixed cultures with Pelobacter carbinolicus and with Geobacter metallireducens are examined more intensively :

  • G. metallireducens (family Geobacteraceae ) transfers electrons to M. barkeri , so that M. barkeri can use them to reduce carbon dioxide.

The two partners named here belong to the same order , Desulfuromonadales . One relationship (“ P. carbinolicus → H 2 → M. barkeri ”) is called HIT (H 2 interspecies transfer) and the other relationship (“ G. metallireducens → e - → M. barkeri ”) is called DIET (Direct interspecies electron transfer ) called.

To compare the two relationships, ethanol was used as the substrate ; The investigations showed that the methane-forming partner, M. barkeri , reacts differently to the availability of hydrogen than to the transfer of electrons. When using hydrogen (HIT), the genes that generally promote protein synthesis and methanogenesis were preferentially expressed , while when using electrons (DIET), genes that affect transmembrane proteins and proteins associated with the S-layer were expressed and those dealing with the biosynthesis of cofactors and prosthetic groups .

These results suggest that the path taken by M. barkeri to reduce carbon dioxide (to methane) by electron transfer (DIET) is fundamentally different from the path of reduction with the aid of hydrogen (HIT). There was no evidence of “ microbial nanowires ” as used by various bacteria in M. barkeri .

Hypotheses on the role of methanosarcina in geological history

Evolution hypothesis

In 2004 Freitas et al. the discovery of two globins in M. acetivorans and another archaeon, Aeropyrum pernix , which they believed to be predecessor versions of hemoglobin and therefore called protoglobins. There are several press releases on this subject. The protoglobins of the archaea bind as much oxygen as the hemoglobin of the vertebrates. In M. acetivorans , they should allow the removal of unwanted oxygen that would otherwise be toxic to this anaerobic organism . Protoglobins may thus have paved the way for the development of later life forms that are dependent on oxygen. After free oxygen was in the earth's atmosphere , the ability to process oxygen led to the widespread distribution of life and is one of the most fundamental stages of evolution of life on earth.

Inspired by the way M. acetivorans converts carbon monoxide into acetate, a team of Penn State researchers proposed a new “ thermodynamic theory of evolution ” (press release), which was published in June 2006. The basis for the new theory is the assumption that early "protocells" may have used primitive enzymes to generate energy , and acetate was excreted. Two theories discussed previously revolved around carbon fixation : the “ heterotrophic ” theory of early evolution, in which the primordial soup of simple molecules would have arisen from non-biological processes, and the “ chemoautotrophic ” theory, in which the earliest forms of life formed the simple molecules would have. The new theory assumed that the metabolic pathways actually originated first to produce energy and only then evolved to fix carbon. The scientists also proposed mechanisms that would enable a mineral-bound protocell (= precursor of a real cell ) to develop into a free-living cell if the same pathways were developed that initially only served to generate energy. As a result, the cell would have been capable of an acetate-to-methane metabolism . It was believed that M. acetivorans was one of the earliest life forms on earth, a direct descendant of the early protocells.

End Permian mass extinction hypothesis

Rothman et al. hypothesized in 2014 that methane production by Methanosarcina was possibly the main cause of the mass extinction at the Permian-Triassic border . There are various press releases on this topic.

The main cause of species extinction on the Permian-Triassic border is generally considered to be volcanism , which appeared with a series of massive volcanic eruptions over a period of 165,000 to 600,000 years. Evidence for the volcanic eruptions are the up to 3000 meters thick flood basalt deposits of the Siberian Trapps , which were formed during the period in question and which covered an area of ​​around 7 million km².

The Rothman et al. The theory put forward says that although volcanism was a trigger of the catastrophe, it was not the immediate cause of the mass extinction. The cause is seen less as the impairment of the living world by the volcanic gases themselves, but more as the resulting possibilities for Methanosarcina . Proponents of the Methanosarcina theory argue, among other things, that their theory better explains the composition of carbon isotopes in the sediment layers towards the end of the Permian than those theories that directly blame the volcanic eruptions in Siberia.

Using genetic analyzes of about 50 methanosarcina - genomes we concluded that these microbes, or their ancestors, had probably acquired the ability approximately 240 ± 41 million years, acetate using new enzymes to convert it into methane, which in would correspond roughly to the time of mass extinction 252 million years ago. The genes for these new enzymes (acetate kinase and phosphoacetyltransferase to activate acetic acid) could have been obtained from the ancestor of Methanosarcina by gene transfer from a cellulose-degrading bacterium.

Furthermore, the volcanic eruptions made nickel available. The nickel (a nickel for the cofactor F430 tetrapyrrole - coenzyme ) is required together with a reductase ( methyl coenzyme M reductase catalyzes the last step in the formation of methane).

The scientists concluded that the new genes, along with widespread organic carbon deposits in the ocean and abundant nickel supply, dramatically increased Methanosarcina populations. According to the theory, this led to the release of copious amounts of methane as waste. Then some of the methane would have been broken down into carbon dioxide by other organisms , consuming oxygen . The oxygen content in the ocean would have decreased drastically and the acidity increased at the same time. The climate zones of the earth have experienced a significant change due to the release of the greenhouse gases methane and carbon dioxide into the atmosphere and simultaneously rising temperatures. It is estimated that 70% of shellfish died out of the acidification of the oceans due to the overgrowth of methanosarcina . Rothman et al. summarized their views roughly as follows:

  • Our fundamental observations, a super-exponential carbon cycle breakout, the emergence of efficient acetoclastic methanogenesis, and an increase in nickel availability, appear to be directly related to several features of end-Permian environmental changes: Siberian volcanism, marine anoxia, and the Ocean acidification . A single horizontal gene transfer triggered a biogeochemical change, massive volcanism acted as a catalyst, and the resulting expansion of the acetoclastic methanosarcina affected the CO 2 and O 2 concentrations. The resulting biogeochemical disturbances were likely to be extensive. For example, anaerobic methane oxidation could have increased sulphide levels, potentially leading to a toxic release of hydrogen sulphide into the atmosphere that caused extinction on land. Although such implications remain speculative, our work illustrates the extraordinary sensitivity of the Earth system to the development of microbial life.

Importance to humans

Technical applications

The simplest way to use methane formation by microorganisms is to fill a container with basically suitable waste, to shield the oxygen-containing air and to collect the fermentation gases that arise . The resulting gas is then burned for heating. In detail, the efficient technical use of methanogenesis is more complicated and requires, among other things, knowledge of the microorganisms involved.

For example, it has been observed that in digesters with sludge as a substrate, the methane-producing microbial community, usually Methanosaetaceae , is dominated, while plants for solid waste that are operated with manure are subsequently predominantly colonized by Methanosarcinaceae . The biogas yield depends heavily on the type of substrate used and the process sequences and conditions that are tailored to it.

In 2011 it was shown that M. barkeri is likely to make a major contribution to decomposition in landfills compared to other methane generators; on a laboratory scale, the microbe, which can survive in low pH environments, has been found to consume the acids , thereby raising the pH and improving methane production. The researchers suggested their results could help advance the development of uses for methane as an alternative energy source (press release).

Another school of thought is the use of genetic engineering . Ways were sought to make more extensive use of Methanosarcina's capabilities for methane production. In 2010, for example, a gene from the bacterium Pseudomonas veronii was introduced into the archaeon Methanosarcina acetivorans with the help of a plasmid , which enabled the modified M. acetivorans strain to break down esters . The University of Arkansas researchers argued that bioengineering could enable more efficient conversion of biomass to methane gas for power generation (press release).

Depending on which result is in focus, the conversion of methane that has been produced in the meantime into another product could also be of interest (“reverse methanogenesis”). Genes for methyl-CoM reductase , which originated from an anaerobic , methanotrophic and non- cultivatable archaea population (ANME-1), were transferred to M. acetivorans and expressed there , whereby the manipulated M. acetivorans strain to methane three times faster Acetate converted as the parent strain.

Especially for M. barkeri was methanogenesis by electron transfer examined (eg. As in Syntrophien with DIET, direct interspecies electron transfer). However, a review article (2018) found that applications in this regard (bioelectrochemical methanogenesis) for all methane generators (and thus also for methanosarcina ) are still on a laboratory scale.

medicine

The methanogenic archaea are not known to be pathogenic germs and are therefore rarely of any significance for medicine . Nevertheless, they colonize anaerobic spaces. In 2003, for example, an unspecified Methanosarcina species was found in a patient's periodontal pocket .

Databases

Remarks

  1. ↑ a b The acetate kinase (En: Acetate kinase ), Expasy-Code EC 2.7.2.1 ( https://enzyme.expasy.org/EC/2.7.2.1 ) implements the reaction ATP + acetate = ADP + acetyl phosphate. Accepted name for EC 2.7.2.1: "Acetate kinase"; [Alternative names: Acetate kinase (phosphorylating), Acetic kinase, Acetokinase, AK]. Acetyl phosphate is an acid anhydride made from acetic acid and phosphoric acid .
  2. ↑ a b The acetic acid (acetate) can only be in the metabolism be used if it is in a so-called activated form, eg. B. as acetyl phosphate , which can be caused by the enzyme acetate kinase . The kinase cleaves an energy-rich compound (e.g. ATP ) and transfers a phosphoric acid group. This creates a high-energy, " activated" connection . In the specific case, this is acetyl phosphate, an acid anhydride that consists of the acetic acid residue (acetyl residue) and a phosphoric acid residue (phosphate residue). Another example of an "activated" acid radical is acetyl coenzyme A .
  3. ↑ a b The Phophatacetyltransferase (En: Phosphate acetyltransferase ), Expasy code EC 2.3.1.8 ( https://enzyme.expasy.org/EC/2.3.1.8 ) is an enzyme that the reaction acetyl-CoA + phosphate =  CoA + Converts acetyl phosphate. Accepted name for EC 2.3.1.8: "Phosphate acetyltransferase"; (Alternative names: phosphoacylase, phosphotransacetylase). Acetyl phosphate is an acid anhydride made from acetic acid and phosphoric acid .
  4. ↑ The acetyl-CoA synthetase  (En: Acetyl-CoA synthetase ), Expasy-Code EC 6.2.1.1 ( https://enzyme.expasy.org/EC/6.2.1.1 ) is an enzyme that the reaction ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA converts. Accepted name for EC 6.2.1.1: "Acetate - CoA ligase"; (Alternative names: Acetate thiokinase, Acetyl-activating enzyme, Acetyl-CoA synthase, Acetyl-CoA synthetase, Acyl-activating enzyme).
  5. ↑ a b Methanosarcina barkeri , type strain DSM 800 in the German Collection of Microorganisms and Cell Cultures (DSMZ), accessed 2019-09: https://www.dsmz.de/catalogues/details/culture/DSM-800.html .
  6. ↑ "anaerobic methanotrophic archaeal population 1" (ANME-1) from sediment from the Black Sea ; Methanotrophy is the recovery of methane
  7. ^ In Robichaux et al. ( 2003 , PMID 12432465 ): "... collected from a patient with type IV periodontal pocket (the periodontal pocket is a space bounded by the tooth on one side and by ulcerated epithelium lining the soft tissue wall on the other)." - translation :. ... removed "from a patient with a periodontal pocket of type IV ( The periodontal pocket is a region on a side of the tooth is limited and on the other side by a geschwürten [ ulcers ] epithelium that lines the soft tissue wall .) "

Individual evidence

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