Methane generator

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Microorganisms whose energy metabolism produces methane ( methanogenesis ) are referred to as methane generators or methanogens ; According to current knowledge, all methane producers belong to the archaea .

For historical reasons, names were coined in connection with methane generators that integrate the word "bacterium" (or a word form of it), although no methane generator belongs to the domain of bacteria . This applies to previously used terms such as B. to “methane bacteria”, but also to names that are valid today, such as the genus Methanobacterium and the class Methanobacteria (see section #Definition of terms ).

Physiology, ecology

The methane generators (methanogens) use exergonic (energy releasing) methanogenesis as an energy source. Some hydrogen oxidizing methanogens are autotrophic . They use carbon dioxide (CO 2 ) as the only carbon source in the synthesis of all cellular components ( anabolism ). They assimilate CO 2 via the acetyl-CoA pathway .

A distinction is made between acetate-splitting methanogens and H 2 -oxidizing methanogens. Acetate-splitting methanogens can form methane from compounds containing methyl groups by splitting off the methyl group and reducing it to methane. They have the coenzyme methanophenazine required for this . The genus Methanosarcina belongs to them . H 2 -oxidizing methanogens form methane by reducing CO 2 with hydrogen to methane and water and by converting formic acid (HCOOH); they do not have methanophenazine. They include the genera Methanococcus , Methanobacterium and Methanopyrus .

The methane generators are strictly anaerobic and metabolize at different temperatures. Some species metabolize around 0 ° C (e.g. Methanobacterium arcticum ), many at medium temperatures (e.g. Methanobacterium formicicum , Methanobrevibacter smithii and Methanosarcina barkeri ), while other species can grow at high temperatures (e.g. Methanothermobacter thermautotrophicus at 75 ° C and Methanocaldococcus jannaschii at 86 ° C). Methanopyrus kandleri can still grow even at 110 ° C. Most methanogens require anoxic , pH- neutral or slightly alkaline environment with at least 50% water. However, there are species that can cope with a low pH (e.g. Methanosarcina barkeri ) or prefer a high pH (e.g. Methanobacterium alcaliphilum ). Anoxic water sediments, soils saturated or flooded with water (e.g. moors and rice fields), manure , liquid manure and the digestive tract of ruminants are particularly good habitats for methanogens, where they find nitrogen compounds, minerals and trace elements that are important for them . Inhibitors for methane builders are organic acids , disinfectants and oxygen .

Other habitats of methane producers are the large intestines of vertebrates , the digestive tract of termites , and the sludge digestion tanks of wastewater treatment and biogas plants.

The methane generators are at the last point in the anaerobic food chain, in which various material conversions take place. In the end, methane is formed through the activity of methane generators.

Taxonomy

The methane generators are not a single taxon , since their commonality of practicing methanogenesis does not have to be automatically linked to phylogenetic relationships and modern taxonomy seeks to map the relationships. Nevertheless, methanogenesis requires physiological properties that make it likely that there is a similar genetics or relationship between different methane generators .

The methane-producing microorganisms used to be called "methane bacteria", a term that has become ambiguous due to the increase in knowledge. There is a risk of confusion, e.g. B. with the class Methanobacteria (see section #Definition of terms ).

When it was not yet possible to map relationships within the taxonomy, Barker (1956) proposed the Methanobacteriacaea family for classifying all methanogens known at the time.

Methods for analyzing kinship relationships were later developed, which were developed in 1979 by Balch et al. could be applied. At that time, the known methane generators were compared with one another, but not yet with non-methane generators. Families and first orders with methanogens were established.

As early as 1986 it became clear that methane generators are not monophyletic , since an order with methanogens was more closely related to an order with non-methane generators than to other methane generators.

In 2001, the first were classes of archaea within the department euryarchaeota erected, containing the methanogens. These taxonomic classes were confirmed in 2002 according to the nomenclature rules .

Up to 2002 five orders with methane generators (Methanobacteriales, Methanococcales, Methanopyrales, Methanomicrobiales and Methanosarcinales) were recognized. In 2008 the sixth order Methanocellales was added. A seventh order with methane generators, Methanomassiliicoccales, was described in 2013. This order, like the six orders mentioned above, belongs to the department of the Euryarchaeota .

The seventh order (Methanomassiliicoccales; Iino et al. 2013) was placed in the class Thermoplasmata when it was described. Thus, the Methanomassiliicoccales were the first order with methanogens, which was placed in a class that previously did not include methanogens.

After the description of the Methanomassiliicoccales, further methane generators were described both in the only department of Euryarchaeota (e.g. order Methanonatronarchaeales; et al. 2018) and in other departments of the archaea (see below).

In 2005, two groups of methane generators were defined that were less related to each other than to non-methane generators; these were the class I and the class II methanogens. The "Class I methanogens" and the "Class II methanogens" were not defined as taxonomic classes according to the nomenclature rules, but as intersections of physiological and phylogenetic classification. At that time methanogens were only known within the Euryarchaeota department.

With the growing number of known archaea and the advances in gene analysis, it became possible in 2015 to add more suitable genes to the usual 16S rRNA genes in order to carry out a more in-depth comparison of the relationships. As a result, two clades were defined within the Euryarchaeota department , which were called "Superclass Methanomonada" and "Superclass Diaforarchaea". The clade "Methanomonada" and the "Class I methanogens" appeared congruent in terms of their members. Furthermore, according to this phylogenetic analysis, the family tree of the Euryarchaeota had a "branch with two branches" (a clade with two subclades), with one branch (or a subclade) representing the "superclass Diaforarchaeota", which had no methanogens, while the other branch the members of the "class II methanogens" and other archaea without methanogenesis properties. With regard to taxonomic orders, three were represented in the "Class I methanogens" (Methanobacteriales, Methanococcales and Methanopyrales) and three others in the "Class II methanogens" (Methanocellales, Methanomicrobiales and Methanosarcinales). The seventh order with methanogenic Euryarchaeota, Methanomassiliicoccales, was not recorded in 2015.

In addition to the methane generators within the phylum Euryarchaeota, archaea with methane metabolism were found in new kin groups, which were named Phylum Bathyarchaeota in 2014 and Phylum Verstraetearchaeota in 2016. Before being named, the Bathyarchaeota were referred to as MCG ( Miscellaneous Crenarchaeota group : diverse Crenarchaeota group), because previously only two phyla of the Archaea were assumed (Euryarchaeota and Crenarchaeota ). Within the Bathyarchaeota, or within the "diverse Crenarchaeota group", there are no genera or species with names, etc. a. because the identifications have been made by indirect examination of genome segments rather than by isolating culture strains. The Verstraetearchaeota have at least candidates.

In addition to methanogenesis, there are also other types of methane metabolism (e.g. anaerobic methane oxidation ) and it was therefore proposed in 2016 that methane production should not be viewed in isolation, but rather as an aspect of a coherent methane metabolism. The focus of consideration was the so-called Wood – Ljungdahl path , which occurs in various ways in archaea and bacteria and in which, under anaerobic conditions, carbon dioxide can be reduced with the help of hydrogen . In archaea, methane is produced (hydrogenotrophic methanogenesis). The core idea of ​​the overview work is that hydrogenotrophic methanogenesis could have been the starting point for the archaea and that modifications of the universal enzyme sets (or genes) during evolution lead to a loss or to a reinterpretation (e.g. anaerobic Methane oxidation).

The idea of ​​a uniform starting point was taken up in 2019 and a comprehensive comparison of genes of methane metabolism in archaea in the different branches of this domain was carried out. The investigation supported the assumption that there might have been an evolutionary origin of the archaea with hydrogenotrophic methanogenesis, u. a. This is because the complete hydrogenotrophic methanogenesis pathway could be found in both the Euryarchaeota and the Verstraetearchaeota, suggesting that the common ancestor of these distantly related groups already possessed this metabolic pathway. On the other hand, horizontal gene transfer must not be overlooked, which makes it possible for organisms to have genes that they did not inherit from their ancestors.

Definition of terms

"Methane bacteria" and methane producers

As a result of the increase in knowledge, the term methane bacteria ” became ambiguous, so that its use today is seldom sensible and in many contexts incorrect. 

The term was previously used for methane generators: "Methane bacteria" referred to two aspects that later had to be seen separately:

  • methane formation and
  • the taxonomic classification.

In 1956, Barker described the methane producers as the physiological group “methane bacteria” (ie “methane bacteria”) and said that they could well be described as the physiological family Methanobacteriaceae . At that time the term “bacteria” (or “bacteria”) was used in two meanings:

  1. to denote all microbes without a real cell nucleus , since the rod (lat. bacterium) is a characteristic cell shape in this group (which is now called prokaryotes ) and
  2. to denote those microbes without a real nucleus, in which the cells are actually rod-shaped .

Barker (1956) used “methane bacteria” to mean that he meant all microbes without a real nucleus that produce methane; regardless of whether it is rod-shaped or not (from today's perspective: prokaryotes that produce methane).

At that time there were hardly any better classification criteria than morphological and physiological, and Barker used a classification in which physiology (methanogenesis) was the overriding criterion and morphology (cell shape) was the subordinate criterion.

This classification was arbitrary:

  • the family ( Methanobacteriaceae ) was placed according to the metabolic end product ( methane ),
  • The genera were classified according to the basic cell shape (rod or ball) and the presence of a special feature (sporulation and aggregation of cells), so that there were four genera ( Methanobacterium : rod-shaped cells that do not sporulate; Methanobacillus : rod-shaped cells that form spores can; Methanococcus : spherical [approximately spherical] cells that do not form cell aggregates; Methanosarcina : spherical cells that form cell aggregates [packets]) and
  • the species were delimited according to the substrates whose metabolic utilization could be observed (e.g. Methanosarcina barkerii : methanol , acetate , carbon monoxide , hydrogen ).

In 1977 Woese and Fox presented three basic lineages of living beings: “eubacteria”, “archaebacteria” and “urkaryotes”. From now on, in addition to the two main meanings of the term “bacteria”, which was used synonymously with the name “ Prokaryotae ” (all microbes without a real cell nucleus) and only referred to the rod-shaped “ Prokaryotae ”, there were other meanings. From now on there were “typical bacteria” (“eubacteria”) and “ancient bacteria” (“archaebacteria”). Of the new lineage “archaebacteria”, only methane generators could be examined at the time of publication.

Two years later, the methane generators by Balch et al. (1979) reevaluated their relationship with the method of Woese and Fox (1977). Shortly thereafter, the International Association of Microbiological Societies ( IUMS ) published Approved Lists, 1980, and new names from the work Balch et al. (1979) validated (1981).

With the addition of new taxa, the possibility of using the term "methane bacteria" or "methane bacteria" clearly for methane producers has been severely restricted. The name Methanobacteriaceae , which Barker had used synonymously with “methane bacteria”, became the recognized name of a family ( Methanobacteriaceae Barker 1956 ) that was part of an order ( Methanobacteriales Balch & Wolfe 1981 ) that was among other taxa in which methane generators were found occurred (e.g. next to the order Methanococcales Balch & Wolfe 1981 ). Thus the former assignment could:

  • Methane generator = Methanobacteriaceae = "methane bacteria",

which could be derived from Barker (1956) no longer work.

In 1990 a work by Woese et al. in which the idea of ​​the three basic lineages of living beings according to Woese and Fox (1977) was taken up and in which the domains Archaea , Bacteria and Eucarya were published. In 1992 a revision of the nomenclature set of rules for microbes without a real nucleus was published ( Bacteriological Code , 1990 revision).

On the one hand there were more and more names for fundamental lineages and on the other hand the rank of taxa with recognized names remained limited to the class; On the one hand, you needed new terms to represent similarities and differences in relation to relationships, on the other hand, you needed stability in the terms. Therefore, the use of names that integrate the words “methane” and “bacteria” could not be avoided.

In 2001 classes were established (e.g. Methanobacteria and Methanococci) that contained methanogens and were activated in 2002. In case of doubt, the methanobacteria class in particular should best be given by its full name ( Methanobacteria Boone 2002 ). Methanobacteria could be translated as “methane bacteria”.

In summary, the homonym “methane bacteria” (or “methane bacteria”) can e.g. B. mean the following:

  • several members (species, strains, colonies, etc.) of the genus Methanobacterium ,
  • all rod-shaped (bacterial) methane generators,
  • all methane generators ("bacteria" as a synonym for all prokaryotes , e.g. Barker 1956)
  • the Methanobacteriaceae family (Barker 1956),
  • the class Methanobacteria (as a common name ).

Methanobacteria and methane producers

The Methanobacteria Boone 2002 class is special in relation to methane generators in that the translation would mean “methane bacteria” (or “methanobacteria”), a designation that can be confused. Names that integrate the words “methane” and “bacterium” (or word forms) tend to be ambiguous (see section # “Methane bacteria” and methane producers ).

Ultimately, the name of the class, "Methanobacteri a ", was derived from the name of the basic genus, "Methanobacteri um ". The class contains other taxa whose names differ only in the ending (order "Methanobacteri ales " and family "Methanobacteri aceae "). The character string "Methanobacteri" is the same for all nested taxa .

Methanobacteria
Systematics
Domain : Archaea (Archaea)
Department : Euryarchaeota
Class : Methanobacteria
Scientific name
Methanobacteria
Boone 2002

In its description (2001), the class Methanobacteria was placed in the phylum (or in the department) Euryarchaeota, within the domain Archaea and operated in 2002. At the time of their description, the Methanobacteria only contained methanogens.

The class Methanobacteria Boone 2002 has the order Methanobacteriales Balch & Wolfe 1981 as type . The order (Methanobacteriales ) and the family Methanobacteriaceae Barker 1956 anchored in it each have the genus Methanobacterium Kluyver & van Niel 1936 as a type.

Historical list

  • Kluyver & van Niel (1936) - Description of the genus Methanobacterium .
  • Barker (1956) - Description of methane generators as the physiological group “methane bacteria” (“methane bacteria”) or as the family Methanobacteriaceae .
  • Balch et al. (1979) - Systematic reassessment of the group of methane generators; on the basis of 16S-RNA analyzes u. a. the new order Methanobacteriales established and there the family Methanobacteriaceae and the genus Methanobacterium were classified.
  • IUMS (1980) - Publication of the "Approved Lists" (1980) for the use of names, etc. a. For:
    • " Methanobacteriaceae Barker 1956",
    • " Methanobacterium Kluyver & van Niel 1936".
  • IUMS (1981) - List number 6 for the validation of new names or new name combinations, etc. a. for the
    • new order " Methanobacteriales Balch & Wolfe 1981".
  • Euzéby & Tindall (2001) - Request for an opinion on the type of order in nomenclature.
  • Boone (2001) - Effective publication on the new class Methanobacteria within the Phylum Euryarchaeota in the Archaea domain.
  • IUMS (2002) - validation list number 85. Confirmation of new names, etc. a. for the
    • new class " Methanobacteria Boone 2002".
  • IUMS (2005) - Opinion number 79 on the type of an order in the nomenclature, u. a. for the
    • Order Methanobacteriales with the type genus Methanobacterium .

literature

  • Lexicon of Biology. Volume 9. Spectrum Academic Publishing House, Heidelberg 2002, ISBN 3-8274-0334-0 .

Remarks

  1. In Bapteste et al. (2005, PMID 15876569 ) was reproduced in connection with the work by Woese & Olsen (1986, PMID 11542063 ) that it was already known in 1986 through analysis of the 16S rRNA genes that the methane generators are not monophyletic because the methane-forming order methanomicrobiales at that time was narrower was related to the extremely halophilic, non-methanogenic order Halobacteriales than to other methane generators.
  2. The order Methanomassiliicoccales was developed by Iino et al. (2013, doi: 10.1264 / jsme2.ME12189 ) and placed within the Thermoplasmata class . The order was confirmed with the type genus Methanomassiliicoccus ( IUMS 2013, doi: 10.1099 / ijs.0.058222-0 ). The description of the genus with its type species Methanomassiliicoccus luminyensis was carried out in 2012 by Dridi et al. ( doi: 10.1099 / ijs.0.033712-0 ) and both have been confirmed ( IUMS 2012, doi: 10.1099 / ijs.0.048033-0 ).
  3. Candidates for names within the phylum Verstraetearchaeota according to Meng et al. (2016, PMID 24108328 ): Genus Methanomethylicus with the species M. mesodigestum and M. oleusabulum , genus Methanosuratus with the species M. petracarbonis , family Methanomethyliaceae, order Methanomethyliales, class Methanomethylia.
  4. Typical bacteria : the authors (Woese & Fox, 1977, PMID 270744 ) saw the “ eubacteria ” as typical and used the prefix “ eu ” (“... contains all of the typical bacteria so far characterized, ... It is appropriate to call this ... eubacteria ”).
  5. Ancient bacteria : The methanogenic phenotype of the “ archaebacteria ” made the authors (Woese & Fox, 1977, PMID 270744 ) think of an ancient geological epoch (“The apparent antiquity of the methanogenic phenotype… to exist on earth 3-4 billion years ago) … To name this… archaebacteria ”).

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  34. The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Prococomicrobiales, Methanomicrobiales are thema, Halobanaocolcus, Prochromicrobiales, Methanomicrobiales are thema, Halobanacus and Procomicrobiales, Methanomicrobiales , Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79 . In: Judicial Commission of the International Committee on Systematics of Prokaryotes (Ed.): International Journal of Systematic and Evolutionary Microbiology . tape 55 , Pt 1, January 2005, ISSN  1466-5026 , p. 517-518 , doi : 10.1099 / ijs.0.63548-0 , PMID 15653928 .