Diversity of Archaea (General Microbiology) - Fall 2023 PDF

General Microbiology L: 11- Diversity of Archaea Fall 2023 Diversity of Archaea We now consider organisms in the domain Archaea. A phylogenetic tree of Archaea is shown in Figure 1. The tree, based on comparative sequences o...

General Microbiology L: 11- Diversity of Archaea Fall 2023 Diversity of Archaea We now consider organisms in the domain Archaea. A phylogenetic tree of Archaea is shown in Figure 1. The tree, based on comparative sequences of ribosomal proteins, reveals several phyla, including the Euryarchaeota, Crenarchaeota, Thaumarchaeota, Korarchaeota, and Nanoarchaeota. The exact ancestry of these groups remains a contentious issue, and phylogenetic trees constructed from 16S ribosomal RNA gene sequences often conflict with those made using other genomic locations. The evolutionary history of the Archaea is ancient and complex, involving horizontal gene transfers within and between phyla. Common features shared by all Archaea include their ether- linked lipids, their lack of peptidoglycan in cell walls, and their structurally complex RNA polymerases, which resemble those of Eukarya. But beyond this, Archaea show enormous phenotypic diversity. Archaea include species that carry out chemoorganotrophic or chemolithotrophic metabolisms, and both aerobic and anaerobic species are common. Chemoorganotrophy is widespread among Archaea, and fermentations and anaerobic respirations are common. Chemolithotrophy is also well established in the Archaea, with H2 being a common electron donor. Anaerobic respiration, especially forms employing elemental sulfur (S0) as an electron acceptor, is prevalent among the Archaea, especially Crenarchaeota. By contrast, aerobic respiration occurs widely in Thaumarchaeota and is common among a few groups of Euryarchaeota but is characteristic of only a few species of Crenarchaeota. Many metabolic features of archaeal species are also found in Bacteria but others are unique to Archaea. Methanogens, for example, are Euryarchaeota that conserve energy from the production of methane. Methanogenesis is a globally important process that is only present in archaea. Archaea are also well known for containing many species of extremophiles, including species that are hyperthermophiles (organisms with growth temperature optima above 80°C), halophiles, and acidophiles. However, a great many species in the Euryarchaeota and most Thaumarchaeota are not extremophiles and are found in soils, sediments, oceans, lakes, in association with animals, and even in the human gut. 1 General Microbiology L: 11- Diversity of Archaea Fall 2023 Figure 1. Detailed phylogenetic tree of the Archaea based on comparisons of ribosomal proteins from sequenced genomes. Each of the five archaeal phyla is indicated in a different color. The Korarchaeota and Nanoarchaeota are each represented by only a single known species. 1. The phylum Euryarchaeota Euryarchaeota comprise a large and physiologically diverse group of Archaea. This phylum includes methanogens as well as many genera of extremely halophilic (salt-loving) Archaea. As a study in physiological contrasts, these two groups are remarkable: Methanogens are the strictest of anaerobes while extreme halophiles are primarily obligate aerobes. Other groups of euryarchaeotes include the hyperthermophiles Thermococcus and Pyrococcus, the hyperthermophilic methanogen Methanopyrus, and the cell wall–less Thermoplasma, an organism phenotypically similar to the mycoplasmas. We begin our review of Euryarchaeota by reviewing the halophilic Archaea. 1.1 Extremely Halophilic Archaea Key Genera: Halobacterium, Haloferax, Natronobacterium Extremely halophilic Archaea, often called the “haloarchaea,” are a diverse group that inhabits environments high in salt. These include naturally salty environments, such as solar salt evaporation ponds and salt lakes, and artificial saline habitats such as the surfaces of heavily 2 General Microbiology L: 11- Diversity of Archaea Fall 2023 salted foods, for example, certain fish and meats. Such salty habitats are called hypersaline. The term extreme halophile is used to indicate that these organisms are not only halophilic, but that their requirement for salt is very high, in some cases at levels near saturation. An organism is considered an extreme halophile if it requires 1.5 M (about 9%) or more sodium chloride (NaCl) for growth. Most species of extreme halophiles require 2–4 M NaCl (12–23%) for optimal growth. Virtually all extreme halophiles can grow at 5.5 M NaCl (32%, the limit of saturation for NaCl), although some species grow very slowly at this salinity. Some phylogenetic relatives of extremely halophilic Archaea, for example species of Haloferax and Natronobacterium, are able to grow at much lower salinities, such as at or near that of seawater (about 2.5% NaCl); nevertheless, these organisms are phylogenetic relatives of other extreme halophiles. 1.2 Methanogenic Archaea Key Genera: Methanobacterium, Methanocaldococcus, Methanosarcina Many Euryarchaeota are methanogens, microorganisms that produce methane (CH4) as an integral part of their energy metabolism (methane production is called methanogenesis). Methanogenesis is the terminal step in the biodegradation of organic matter in many anoxic habitats in nature. Table 1 lists the major sources of biogenic methane in nature. Diversity and Physiology of Methanogens Methanogens show a variety of morphologies. Their taxonomy is based on both phenotypic and phylogenetic analyses, with several taxonomic orders being recognized, each of which contains one or more genera. Methanogens show a diversity of cell wall chemistries. These include the pseudomurein, the protein or glycoprotein walls, and the S-layer walls. Physiologically, methanogens are obligate anaerobes, and strict anoxic techniques are necessary to culture them. Most methanogens are mesophilic and nonhalophilic, although species that grow optimally at very high or very low temperatures, at very high salt concentrations, or at extremes of pH, have also been described. Several substrates can be converted to CH4 by methanogens. 3 General Microbiology L: 11- Diversity of Archaea Fall 2023 Interestingly, these substrates do not include such common compounds as glucose and organic or fatty acids (other than acetate and pyruvate). Compounds such as glucose can be converted to CH4, but only in reactions in which methanogens and other anaerobes cooperate. Three classes of compounds make up the list of methanogenic substrates shown in Table 2. These are CO2-type substrates, methylated substrates, and acetate. CO2-type substrates include CO2 itself, which is reduced to CH4 using H2 as the electron donor. Other substrates of this type include formate (which is CO2 + H2 in combined form) and CO, carbon monoxide. Methylated substrates include methanol (CH3OH) and many others (Table 2). Table 1: Habitats of methanogens 4 General Microbiology L: 11- Diversity of Archaea Fall 2023 Table 2: Substrates converted to methane by various methanogenic Archaea The reactions of methane production are summarized in the following equations: (1a): Fumarate; (1): CO; (2b): CO2: (3b): acetate. 4HC02- + H20 + H --> CH4 + 3HC03- (1a) 1.3 Thermoplasmatales Key Genera: Thermoplasma, Picrophilus, Ferroplasma A phylogenetically distinct line of Archaea contains thermophilic and extremely acidophilic genera: Thermoplasma, Ferroplasma, and Picrophilus. These prokaryotes are among the most acidophilic of all known microorganisms, with Picrophilus being capable of growth even below 5 General Microbiology L: 11- Diversity of Archaea Fall 2023 pH 0. Most are thermophilic as well. These genera also form their own taxonomic order within the Euryarchaeota, the Thermoplasmatales. Species of Thermoplasma are facultative aerobes, growing either aerobically or anaerobically by sulfur respiration. To survive the osmotic stresses of life without a cell wall and to withstand the dual environmental extremes of low pH and high temperature, Thermoplasma has evolved a unique cytoplasmic membrane structure. The membrane contains a lipopolysaccharide- like material called lipoglycan. This substance consists of a tetraether lipid monolayer membrane with mannose and glucose. This molecule constitutes a major fraction of the total lipids of Thermoplasma. The membrane also contains glycoproteins but not sterols. These molecules make the Thermoplasma membrane stable to hot, acidic conditions. 1.4 Archaeoglobales Key Genera: Archaeoglobus, Ferroglobus Archaeoglobus Archaeoglobus was isolated from hot marine sediments near hydrothermal vents. In its metabolism, Archaeoglobus couples the oxidation of H2, lactate, pyruvate, glucose, or complex organic compounds to the reduction of SO42− to H2S. Ferroglobus Ferroglobus is related to Archaeoglobus but is not a sulfate reducer. Instead, Ferroglobus is an iron-oxidizing chemolithotroph, conserving energy from the oxidation of Fe2+ to Fe3+ coupled to the reduction of nitrate (NO3−) to nitrite (NO2 −). Ferroglobus grows autotrophically and can also use H2 or H2S as electron donors in its energy metabolism. Ferroglobus was isolated from a shallow marine hydrothermal vent and grows optimally at 85°C. 6