taxonomy Taxonomy is the practice and science of categorization or classification. A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...

, ''Methanopyrus'' is a

genus Genus ( plural genera ) is a taxonomic rank used in the biological classification of living and fossil organisms as well as viruses. In the hierarchy of biological classification, genus comes above species and below family. In binomial nom ...

of the

Methanopyraceae In taxonomy, the Methanopyraceae are a family of the Methanopyrales. This family contains only one genus, which contains only one species, ''Methanopyrus kandleri''. It is chemolitoautotrophic and its cells are bar-shaped. It can grow comfortabl ...

. ''Methanopyrus'' is a genus of

methanogen Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They are prokaryotic and belong to the domain Archaea. All known methanogens are members of the archaeal phylum Euryarchaeota. Methanogens are c ...

, with a single described species, ''M. kandleri''. It is a rod-shaped hyperthermophile, discovered on the wall of a

black smoker A hydrothermal vent is a fissure on the seabed from which geothermally heated water discharges. They are commonly found near volcanically active places, areas where tectonic plates are moving apart at mid-ocean ridges, ocean basins, and hotspot ...

from the

Gulf of California The Gulf of California ( es, Golfo de California), also known as the Sea of Cortés (''Mar de Cortés'') or Sea of Cortez, or less commonly as the Vermilion Sea (''Mar Bermejo''), is a marginal sea of the Pacific Ocean that separates the Baja C ...

at a depth of 2,000 m, at temperatures of 84–110 °C. Strain 116 was discovered in black smoker fluid of the Kairei hydrothermal field; it can survive and reproduce at 122 °C. ''M. kandleri'' also requires a high ionic concentration (>1 M) in order for growth and cellular activity. Due to the species' high resilience and extreme environment, ''M. kandleri'' is also classified as an

extremophile An extremophile (from Latin ' meaning "extreme" and Greek ' () meaning "love") is an organism that is able to live (or in some cases thrive) in extreme environments, i.e. environments that make survival challenging such as due to extreme tem ...

. It lives in a

hydrogen Hydrogen is the chemical element with the symbol H and atomic number 1. Hydrogen is the lightest element. At standard conditions hydrogen is a gas of diatomic molecules having the formula . It is colorless, odorless, tasteless, non-to ...

carbon dioxide Carbon dioxide ( chemical formula ) is a chemical compound made up of molecules that each have one carbon atom covalently double bonded to two oxygen atoms. It is found in the gas state at room temperature. In the air, carbon dioxide is t ...

rich environment, and like other methanogens reduces the latter to

methane Methane ( , ) is a chemical compound with the chemical formula (one carbon atom bonded to four hydrogen atoms). It is a group-14 hydride, the simplest alkane, and the main constituent of natural gas. The relative abundance of methane ...

. It is placed among the

Euryarchaeota Euryarchaeota (from Ancient Greek ''εὐρύς'' eurús, "broad, wide") is a phylum of archaea. Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines, halobacteria, which survive extr ...

, in its own class.

Microbiological characteristics

Morphology

''Methanopyrus kandleri'' is a rod-shaped,

Gram-positive In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall. Gram-positive bact ...

with an approximate length of 2-14 μm and diameter of 0.5 μm. The cellular membrane of ''M. kandleri'' is unique as it consists of terpenoid lipids, believed to be one of the most primitive lipids and a predecessor to phytanyl di-

ether In organic chemistry, ethers are a class of compounds that contain an ether group—an oxygen atom connected to two alkyl or aryl groups. They have the general formula , where R and R′ represent the alkyl or aryl groups. Ethers can again ...

s found in later archaea. Terpenoid lipids are a group of lipids containing

cholesterol Cholesterol is any of a class of certain organic molecules called lipids. It is a sterol (or modified steroid), a type of lipid. Cholesterol is biosynthesized by all animal cells and is an essential structural component of animal cell memb ...

, hopanoids,

carotenoid Carotenoids (), also called tetraterpenoids, are yellow, orange, and red organic pigments that are produced by plants and algae, as well as several bacteria, and fungi. Carotenoids give the characteristic color to pumpkins, carrots, parsnips, ...

, phytane, and bisphytane. Although terpenoids are the main component of the membrane in ''M. kandleri'', they are more of a supporting structure in

eukaryote Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacter ...

and

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...

. ''M. kandleri'' is motile via polar flagella tufts. ''Methanopyrus kandleri'' has a high concentration of cyclic 2,3-diphosphoglycerate. This compound is often found in hyperthermophile, helping to prevent

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...

denaturation in high temperatures. The increased concentration of cyclic 2,3-diphosphoglycerate protects the methanogen, helping it survive in an environment that many other organisms could not. Beyond this compound to help protect the proteins, ''M. kandleri'' also has a high salt concentration inside its membrane. This increased concentration of salt helps with

enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products ...

stability and promotes activity of the enzymes at higher temperatures.

Metabolism

As a methanogen, ''M. kandleri'' utilizes hydrogen as an electron source and reduces carbon dioxide from the environment into methane, a process known as

methanogenesis 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 ...

. ''M. kandleri'' is a chemolithoautotrophic, obligate

anaerobe An anaerobic organism or anaerobe is any organism that does not require molecular oxygen for growth. It may react negatively or even die if free oxygen is present. In contrast, an aerobic organism (aerobe) is an organism that requires an oxygenate ...

and does not use oxygen as a final electron acceptor.

Habitat

Cultures of ''M. kandleri'' have been isolated from various submarine hydrothermal vents from locations in the Gulf of California, Central Indian Ridge, Mid-Atlantic Ridge, and Iceland. The species was first discovered on the wall of a

from the

at a depth of 2,000 m, at temperatures of 84–110 °C. ''M. kandleri'' can survive up to temperatures of 122 °C, although optimal growth has been determined to be at 98 °C. High internal ionic cell concentrations (>1 M) are required for cell growth and activity. Due to the extremity of environment that ''M. kandleri'' resides in, it is hypothesized that further phylogenetic isolation has occurred due to the exclusivity of the species niche.

Genomic properties

The complete genome of ''Methanopyrus kandleri'' was sequenced by researchers at Fidelity Systems. It was determined to be a GC-rich genome containing 1,694,969

nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecu ...

s of which about 62.1% is

guanine Guanine () ( symbol G or Gua) is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine ( uracil in RNA). In DNA, guanine is paired with cytosine. The guanine nucleoside is ...

cytosine Cytosine () ( symbol C or Cyt) is one of the four nucleobases found in DNA and RNA, along with adenine, guanine, and thymine ( uracil in RNA). It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached ( ...

. The single circular chromosome possesses 1,691 protein-coding genes and 39 RNA genes. The species also possesses a large number of orphan genes, possibly through viral gene transfer.

Future research

''Methanopyrus kandleri'' is also the only species known to have topoisomerase V. Topoisomerase V allows for ''M. kandleri'' to survive in such high temperatures and helps to relax both positively and negatively supercoiled DNA . Topoisomerase V is a unique enzyme because it possesses both topoisomerase and DNA repair activities, specifically multiple DNA repair sites that can act independently of each other even if there is damage to one of the sites on the DNA. Although topoisomerase V is useful in this case, finding other hyperthermophiles that have topoisomerase V has proven difficult. This lack of topoisomerase V in other archaeon has led researchers to believe that the origin of the enzyme in ''M. kandleri'' is a result of viral gene transfer and the unusual amount of orphan genes in the species provides evidence for this theory. Additionally, the evolved cellular responses in ''M. kandleri'' due to its extreme environment has been another subject of research, as scientists look to apply the resilient enzymatic processes for industrial purposes.

References

External links

Type strain of ''Methanopyrus kandleri'' at Bac''Dive'' - the Bacterial Diversity Metadatabase