Diversity of Archaea: Methanogens

Diversity of Archaea

• Archaea share characteristics with Bacteria and Eukarya.
• Archaea are split into five main groups: Euryarchaeota, Crenarchaeota, Thaumarchaeota, Korarchaeota, and Nanoarchaeota.

Crenarchaeota

• Crenarchaeota tend to have slow evolutionary clocks and appear phenotypically homogeneous compared to other archaea.
• Three orders compose this archaea: Desulfurococcales, Sulfolobales, and Thermoproteales.
• Cultured organisms represent a minority of the diversity.
• Uncultured species are encountered through environmental sequence studies.
• The majority are hyperthermophiles, thermophiles, or "extremophiles," but mesophiles or psychrophiles of uncertain physiology have been observed.

Korarchaeota

• Indicated by 16S rDNA sequences from environmental DNA samples.
• Little information is available regarding their corresponding organisms.

Nanoarchaeota

• Nanoarchaeota are nano-sized hyperthermophilic symbionts.
• They grow attached to the surface of an Ignicoccus species.

Distinctive Features of Archaea

• Exhibit extreme thermophilic characteristics in some groups.
• Lipids consist of glycerol ethers of isoprenoids; tetraethers are common.
• Stereochemistry of lipids is 2,3-sn glycerol.
• Cell walls contain protein, glycoprotein, or pseudomurein; murein is absent.
• Antibiotic sensitivity differs from bacteria.
• Unique modes of energy metabolism are present in some groups; examples include bacteriorhodopsin-driven photosynthesis and methanogenesis.

Energy Conservation and Autotrophy in Archaea

• Bioenergetics and intermediary metabolism in species of Archaea are much the same as in Bacteria, with the exception of methanogenesis.
• Several Archaea are chemoorganotrophic utilizing organic compounds as energy sources for growth.
• Chemolithotrophy is also well established, with H₂ as a common electron donor.
• Autotrophy is widespread and occurs by different pathways.
• Carbon dioxide is incorporate via the acetyl-CoA pathway in methanogens and chemolithotrophic hyperthermophiles, or a modification thereof.

Euryarchaeota

• This group is physiologically varied.
• Classes include Extremely Halophilic Archaea, Methanogenic Archaea, Thermoplasmatales, Thermococcales and Methanopyrus, and Archaeoglobales.
• Euryarchaeota are a physiologically diverse group of Archaea that inhabit extreme environments, such as high temperatures, salt concentrations, and acidity.

Methanogenic Archaea

• These are methanogens, whose key genera are Methanobacterium, Methanocaldococcus, and Methanosarcina.
• These microbes produce CH₄ (methane) as an integral part of their energy metabolism.
• Methanogens are strictly anaerobic prokaryotes found in many diverse environments.
• Taxonomy is based on phenotypic and phylogenetic features.
• They are primarily related by their mode of energy metabolism, but diverse in other properties.
• Methanogens are obligate methane-producers, only growing under conditions where methane is formed.

Diversity of Methanogens

• Cell wall chemistry demonstrates diveristy:
  • Pseudomurein in Methanobacterium
  • Methanochondroitin in Methanosarcina
  • Protein or glycoprotein in Methanocaldococcus
  • S-layers in Methanospirillum

Substrates for Methanogens

• Substrates include 11 substrates which can be converted to CH₄ by pure cultures and divided into 3 classes.
• Other compounds, like glucose, can be converted to methane but only in cooperative reactions between methanogens and other anaerobic bacteria.
• All substrates are converted stoichiometrically to methane, and they are obligate anaerobes.
• Three groups/types of energy substrates for growth:
  • Energy substrate (electron donor) is H₂, formate, or certain alcohols, and the electron acceptor is CO₂, which is reduced to methane.
  • The ability to utilize H₂ as an electron donor for CO₂ reduction is almost universal among methanogens; many utilize formate, but utilizing alcohols is less common.
  • Methyl-containing C-1 compounds serve as substrates for a few taxa.
  • Some molecules of the substrate are oxidized to CO₂; the electron acceptors are the remaining methyl groups, which are reduced directly to methane.
  • Methanogenesis from C-1 compounds is common where methyl-containing C-1 compounds are abundant.
  • Acetate is also a major source of methane but is generally limited to a few species of Methanosarcina and Methanosaeta.
  • Methyl carbon of acetate is reduced to methane, and the carboxyl carbon is oxidized to CO₂.
  • Acetate is present in many environments and is common in anoxic freshwater sediments where the catabolism of acetate by other anaerobes is limited by the availability of alternate electron acceptors such as sulphate or nitrate.

Methanogens: Interspecies Electron Transfer

• Methanogens depend on fermentative bacteria to convert a wide range of organic compounds into substrates because of their limited substrate range.
• In environments where organic matter is degraded to CH₄ and CO₂, the methanogenic precursors are predominantly acetate, formate, and H₂ + CO₂.
• The organic matter is initially fermented mainly to volatile organic acids (like formate and acetate), H₂, and CO₂, which methanogens can use.
• Longer-chain volatile organic acids (3C or more) must be metabolized to one or more of these substrates by a specialized group of microbes called syntrophs.
• Syntrophs form methanogenic substrates only in the presence of low concentrations of H₂ or formate.
• When syntrophs are grown in co-cultures with H₂ and formate-utilizing methanogens, the concentrations of H₂ and formate remain low.
• In such co-cultures, syntrophs produce more acetate and less reduced products such as propionate, butyrate, lactate, and ethanol.
• Fermentative bacteria can generally grow without methanogens; however, additional energy is obtained from acetate production when methanogens are present.
• This type of interspecies electron transfer is called non-obligate interspecies electron transfer.

Methanogens: Obligate Syntrophy

• Interspecies electron transfer cannot proceed without the activities of H₂ or formate-utilizing species.
• Obligate syntrophs oxidize compounds such as propionate, longer-chain volatile organic acids, and aromatic compounds.
• Obligate syntrophs must dispose of the electrons by the reduction of protons to H₂ or of CO₂ to formate.
• Obligate syntrophs lack alternative fermentative reactions and cannot produce other reduced organic compounds.
• End-product inhibition prevents the oxidation of the syntrophic substrates when the concentrations of H₂ and formate are high.
• Methanogens keep the concentrations low.

Methanogens: Methanogenesis

• Methanogens contain many novel coenzymes associated with methane synthesis.
• What should be a chemically simple reduction of C-1 compounds to methane is biochemically complex.
• The steps include:
  • Initially, CO₂ is activated to form formylmethanofuran (formyl-MFR).
  • Next, the formyl group is transferred to tetrahydromethanopterin (H₄MPT), where it is reduced to the methylene-H₄MPT then methyl-H₄MPT.
  • Last, the methyl group is transferred to coenzyme M and reduced to methane by the methylreductase system.

Habitats of Methanogens

• Methanogenic bacteria are abundant in habitats where electron acceptors such as O₂, NO₃⁻, Fe³⁺, and SO₄²⁻ are limiting.
• In anoxic environments, the presence of NO₃⁻, Fe³⁺, and SO₄²⁻ inhibits methanogenesis by allowing other organisms to outcompete methanogens for reduced substrates.

Methanogens: Antibiotic Sensitivity

• Methanogens and other Archaea lack sensitivity to most antibiotics.
• They are resistant to many commonly used antibiotics simply because the specific target is not present.
• This is due to differences in the chemical structure of methanogen cell envelopes compared to bacteria.
• Methanogens lack sensitivity to many cell-wall inhibitors.

Methanogens: Cell Wall Structures

• Large differences in cell envelope structure:
  • Pseudomurein is peptidoglycan analogous to bacterial murein.
  • A simple protein cell wall contains a crystalline arrangement of proteins or glycoproteins called an S-layer.
  • The S-layer provides only limited support and cells are osmotically fragile.
  • Heteropolysaccharide has a polysaccharide matrix similar in structure to eukaryotic chondroitin found in connective tissue.
  • The outer protein sheath is surrounded by an electron-dense inner wall of unknown composition and separated by septa or plugs.

Methanogens: Cell Membrane

• Characterized by several unusual lipids and differs from the lipid bilayer of bacteria.
• Most have polar lipids, either diphytanyl-glycerol-diethers or dibiphytanyl-diglycerol-tetraethers.
• Tetraethers appear to span the membrane, with the polar head groups at opposite sides.
• Membranes are arranged in a monolayer with bilayer regions resulting from interspersed diethers.

Methanogens: Applications

• Consortia Preparation involves initial inoculum that are obtained from natural sources like manure, sewage sludge, or freshwater sediment.
• This inoculum is then enriched with the waste material of interest under methanogenic conditions. Mixtures have been obtained for degrading a wide variety of wastes and other materials.
• Examples include: Thermophilic consortia are obtained by performing enrichments at high temperatures and Methanogenic consortia for whey degradation.
• Capable of nearly complete conversion of whey to methane and CO₂ within 5 days.
• Treatment of domestic sewage
• Treatment of industrial waste
• Degradation of xenobiotics: Degradation of common pollutants like halogenated aromatic and aliphatic compounds.
• Methane production from landfills and other waste