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A Microbial Biorealm page on the genus Methanosaeta thermophila
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).
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.
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 determined.
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): 15184-15189. 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 http://www.genomesonline.org/DBs/goldtable.txt 7) http://www.genome.jp/kegg-bin/show_organism?org=mtp 8) ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Methanosaeta_thermophila_PT/ 9) http://genome.jgi-psf.org/draft_microbes/metth/metth.info.html 10) NCBI/RefSeq:NC_008553 http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val =NC_008553 11) Map of Chromosome: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=TaxonCircMaps&page =circMaps&taxon_oid=639633038&pidt=25318.1178126134 12) http://genome.jgi-psf.org/finished_microbes/metth/metth.home.html 13) http://genome.jgi-psf.org/finished_microbes/metth/metth.home.html 14) http://expasy.org/sprot/hamap/METTP.html 15) http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=349307