Methanosaeta thermophila

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A Microbial Biorealm page on the genus Methanosaeta thermophila


Domain: Archaea

                   Phylum:	Euryarchaeota
                     Class:	Methanomicrobia
                     Order:	Methanosarcinales
                   Family:	Methanosaetaceae
                    Genus: 	Methanosaeta
                  Species:     Methanothrix thermophila
     Genus Species Strain:     Methanosaeta thermophila PT
             Name History:	Synonyms: Methanothrix thermophila PT
                                         Methanothrix thermophila DSM 6194 
         Equivalent names:     Methanosaeta thermophila strain PT
                               Methanosaeta thermophila strain PT

Description and Significance

           Methanosaeta thermophila are nonmotile, nonsporulating, and 
 thermophilic, which means they thrive at temperatures of 50ºC or higher.
          This microbe was discovered by a molecular technique using fluorogenic 
 PCR polymerase chain reaction, (which amplifies DNA) to identify its 
 methanotrophic and activity in marine anoxic microbial communities. This was 
 accomplished by identifying and quantifying the mcrA genes. Following 
 amplification, molecular analysis was performed by clone analysis of the 16S 
 rRNA and mcrA genes.  The mcrA genes (encoding the methyl coenzyme M reductase, 
 specific to methanogenic archaea), are specific to the various phylogenetic 
 groups of methanotropic Archaea. Methanosaeta thermophila was identified 
 among the microbial communities in deep sediments and “methane seepages of 
 Omine Ridge in the Nankai Trough accretionary prism,” (1).  
           The addition of Methanosaeta to the methanoarchaeal genome 
 sequence compilation offered an opportunity to gain significant insight into 
 this intricate microbe and the unique use of comparative genomic approaches 
 allows one to address the nature of these specific microbes and their biological 
 influence and capability. Because these microbes are methanogens, they serve 
 an important role as the producers of natural gas and have potential as 
 creators of biofuels (fuels derived from a biomass).

Genome Structure

The Methanosaeta thermophila genome has been entirely sequenced.

 These microbes possess circular chromosomes and do not contain plasmids. 
 (The following genome sequence information is from reference # 11)
        Genome Sequence: RS: NC_008553     
        Genome Sequence Length: 1879471 
        Statistics: Number of nucleotides: 1879471
                    Number of protein genes: 1696
                    Number of RNA genes: 51

Cell Structure and Metabolism

Methanosaeta thermophila is circular (coccus), with one inner membrane
 and one cell wall. This microbe does not interact with other organisms, grows 
 extremely slow, does not contain plasmids, does not possess flagella, but they 
 do however produce gas vacuoles to help them move in aquatic environments. Gas
 vacuoles are cavities within the cytoplasm, which contain a gas similar to that 
 of their surrounding atmosphere. These vacuoles serve as flotation devices 
 because they decrease in size when subjected to increased hydrostatic pressure. 
 So although they are nonmotile, their gas vacuoles allow some degree of 
 flexibility in regards to how much movement they have in aquatic environments.    
      Methanosaeta thermophila obtain their energy as a “thermophilic 
 obligately-aceticlastic methane-producing archaeon,” which means that they 
 produce methane from acetate (4).  Although approximately two-thirds of all 
 methane is derived from the methyl group of acetate, Methanosaeta are able
 to utilize acetate as a substrate for methanogenesis. Methanosarcina is 
 the only other genus of methanoarchaea that are capable of utilizing acetate
 as a substrate, as well as using H2/CO2, dimethylsulfide, and and methanethiol 
 compounds as substrates.  Unlike the faster-growing Methanosarcina, which 
 prefers methylated compounds to acetate, Methanosaeta is a slow-growing 
 specialist that utilizes acetate only.  


       The environment at which Methanosaeta thermophiles are found is 
 aquatic (living and growing in water) and they exhibit optimal growth between
 55-60°C. Although they are present in many environments, such as anaerobic 
 digesters, anaerobic biofilms, sediments, and anaerobic sludges, they are 
 predominantly found in rice paddies, which allow a continuous stream of water 
 to flow through them. Acetate is the most important substrate for 
 methanogenesis in rice paddies and studies have shown that the concentration 
 of acetate in flooded rice paddies is in the 5-100 mM range, and Methanosaeta 
 thermophiles are the predominant acetate-utilizing methanoarchaea in these 
 aquatic rice paddies.   
      Methanosaeta species are the most prevalent methanogenic archaea of 
 the microbial population in numerous environments, including rough sludge 
 digesters, solid wastes, sewage slush,and anaerobic reactors.  During activation 
 of anaerobic bioreactors, Methanosaeta species are widespread due to the 
 high acetate concentration. However, as bioreactors become stable and attain 
 their peak performance, the acetate concentration decreases, as well as the 
 Methanosaeta population.


       Methanosaeta thermophilaare not pathogens and therefore are not disease 
 causing microbes. To this date, there are no known archaea that are pathogens.

Application to Biotechnology

        Methanosaeta thermophila are relevant for biotechnology, energy 
 production, and as major manufacturers as biofuels. As methanogens, M. 
 thermophila are a source of natural gas and can be useful producers of 
 biofuels because they can metabolize acetate into methane by “reducing the 
 methyl group to CH4 with electrons derived from oxidation of the carbonyl  
 group to CO2,” (5). With biofuels, fuel is produced from various resources, 
 such as plants, vegetable oils, and treated municipal and industrial wastes. 
 The use of biofuels as a preservative to petroleum-based fuels can have the 
 effect of burning with less discharge of carbon monoxide and pollutants, 
 helping to produce a cleaner environment. 
        Methanosaeta thermophila are also contributors to bio-gas. Bio-gas 
 is the product of the anaerobic breakdown of organic matter, such as sewage 
 and waste products, by bacteria, which produce a mixture of methane and carbon 
 dioxide. This reaction is important because bio-gasses are used in the 
 generation of hot water and electricity.

Current Research

        Although Methanosaeta continues to be comprehensively studied both
 biochemically and genetically, studies have decreased due to its slow growth
 (up to 12 days doubling time) and lower growth yield than other microbes.  
 One current study of this microbe by Alber, B.E. and Ferry J.G., determined 
 that Methanosaeta thermophila archaea produce a carbonic anhydrase, which 
 is an enzyme that catalyzes the reaction of water with carbon dioxide. The 
 carbonic anhydrase(abbreviated CA) from acetate-grown Methanosaeta 
 thermophila was purified. The molecular mass of the enzyme (CA) was 
 determined via gel filtration chromatography. The results indicated that 
 this particular CA represented a distinct class of CA’s and provided a 
 foundation to determine the unique roles for CA in acetotrophic anaerobes.
        Another study detected central glutamates in the acetate kinase from 
 the Methanosaeta thermophila. Acetate kinase is an enzyme which catalyzes
 the reversible phosphorylation (adding a phosphate group) of acetate. The
 suggested mechanism denoted an unspecified glutamate residue was phosphorylated, 
 and the “alignment of the amino acid sequences for the acetate kinases from 
 E. coli (Bacteria domain), Methanosarcina thermophila (Archaea domain), 
 and four other phylogenetically divergent microbes revealed high identity 
 which included five glutamates,” (9). These glutamates were substituted in
 the M. thermophila enzyme to determine if they were required for catalysis. 
 The substituted enzymes were tagged and created in E. coli and purified by 
 metal affinity chromatography. The substituted enzymes produced undetectable 
 kinase activity.  These results imply that the glutamates in the acetate
 kinase were in fact required for catalysis, which supports the original 
 suggested mechanism.
       A third study explored new methods which permitted genetic analysis 
 within the Archaea domain. Several separately, individually, replicating 
 plasmid shuttle vectors were constructed. These vectors that were created 
 were successful at replication in 9 of the 11 Methanosaeta strains tested. 
 A method was created where DNA was brought in by liposomes, which permitted 
 transformation. During the course of this study, the complete DNA sequence was 


 1) Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T.,
    Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L.,
    Schmutz J.,  Larimer F., Land M., Hauser L., Kyrpides N., Kim E., Smith K.S., 
    Ingram-Smith C., Richardson P.; "Complete sequence of Methanosaeta thermophila 
    PT."; Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
 2) Identification of Essential Glutamates in the Acetate Kinase from 
    Methanosarcina thermophila. Singh-Wissmann K, Ingram-Smith C, Miles RD, Ferry
    JG. J Bacteriol. 1998 Mar; 180(5): 1129-1134.
 3) Carbonic anhydrase is an ancient enzyme widespread in prokaryotes. Smith KS,
    Jakubzick C, Whittam TS, Ferry JG. Proc Natl Acad Sci U S A. 1999 Dec 21; 96(26): 
 4) A carbonic anhydrase from the archaeon Methanosarcina thermophila.
    Alber BE, Ferry JG. Proc Natl Acad Sci U S A. 1994 Jul 19; 91(15): 6909-6913.
 5) A genetic system for Archaea of the genus Methanosarcina: Liposome-mediated 
    transformation and construction of shuttle vectors. Metcalf WW, Zhang JK, 
    Apolinario E, Sowers KR, Wolfe RS. Proc Natl Acad Sci U S A. 1997 Mar 18; 
    94(6): 2626-2631. PMCID: 20139
 6)  NCBI, Joint Genome Institute, Unpublished, October 25, 2006, Richardson P
10) NCBI/RefSeq:NC_008553
11) Map of Chromosome: