BSc 2nd Year Microbiology of Extreme Environments Notes Study Material
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BSc Microbiology of Extreme Environments Notes Study Material
Microorganisms are found under natural conditions in various habitats characterised by different environmental conditions. Microbes indigenous or autochthonous to a particular habitat are capable of survival, growth and metabolic activity within that habitat. Autochthonous microbes occupy a functional position or niche of that ecosystem. Microbes, foreign to a given habitat (transported from somewhere else) do not occupy such niche and are transient members of the microbial community of that ecosystem. Foreign microbes are called allochthonous. Generally autochthonous microbes must possess adaptive features that make them physiologically compatible with the physical, chemical and biological environments of the habitat. They must be functionally and competitively compatible with other organisms of that habitat. Thus, microbes occupying extreme environments such as hot springs, desert soils, and oceans and trenches must possess physiological adaptations that permit them to survive and function under conditions that normally preclude biological activity.
The conditions of extreme environments greatly restrict the range of microbial species that can grow in such habitats. The extremes of environmental conditions that the microbes must be able to tolerate include high temperatures (nearby to boiling water); low temperature (nearby to freezing levels), low acidic pH values, high alkaline pH values, high salt concentrations, low water availability, high irradiation levels, low concentrations of nutrients and high concentrations of toxic compounds. Many microbes that inhabit extreme environments, including hot springs, salt lakes and antarctic desert soils possess specialised adaptive physiological features that permit them to survive and function within the physiochemical constraints of these ecosystems. The membranes and enzymes of microbes of extreme environments often have also distinct modifications that allow them to function under conditions that would inhibit active transport and metabolic activities in organisms lacking these adaptive features.
Adaptive features and conditions of respective habitats occupied by three major groups of archaebacteria – methanogens, halobacteria and thermoacidophiles are considered below.
Members of this group are shown to be phylogenetically related to each other on the basis of analysis of their 16s rRNA molecules, and to be distinct from eubacteria. They are unique in the sense that their cell walls lack murein and in their cell membrane lipids, there are unusual ether linkages. Archaebacteria appear to be primitive bacteria, and as members of the kingdom Archaebacteria, they are considered to be distantly related to other prokaryotes. These are important in evolutionary processes and other phylogenetic relationships.
Three major groups of archaebacteria are distinguished on the basis of metabolic or ecological features: the methanogens, the halophiles, and the thermoacidophiles. The methanogens are distinguished by their unique energy metabolism in which methane is a prominent end product. The halophiles and the thermoacidophiles are distinguished by their habitats: highly saline environment for the former, high temperature and low pH for the latter. However, two of the groups are internally heterogeneous.
Two types of lipid structure are found: glycerol diethers and diglycerol tetraethers. Their hydrocarbon chains are normally the C20 phytane or the C40 biphytane, respectively. Membranes that contain diglycerol dibiphytanyl tetraether probably consist of a monolayer rather than a bilayer, with each lipid molecule spanning the entire membrane. In general, thermoacidophiles contain mainly dibiphytanyl tetraethers; the halophiles mainly diphytanyl diethers. Two different patterns of distribution occur in methanogens; coccoid cells contain only diphytanyl diethers, whereas the rest contain both diphytanyl diethers and dibiphytanyl tetraethers.
 Methanogens (Methane-producing bacteria)
Members represent a highly specialised physiological group. They belong to Methanobacteriaceae (Methanobacterium, Methanobrevibacter); Methanococcaceae (Methanococcus); Methanomicrobiaceae (Methanomicrobium, Methanogenium, Methanospirilham) and Methanosarcinaceae (Methanosarcina). They form methane by reducing CO2 (chemolithotrophs). Methanogens are very strict obligate anaerobes. For methane production, they utilise electrons generated in the oxidation of hydrogen or simple organic compounds such as acetate and methanol. These microbes are unable to use carbohydrates, proteins or other complex organic substrates. The other microbes associated with methanogens maintain the low O2 tensions and provide CO2 and fatty acids methanogens. Such associations are extremely important in the rumen of animals like cows- a major source of atmospheric methane. Some common methanogens are, Methanospirillum hungatei, Methanobacterium thermoautotrophicum, M. soehngenii, Methanobrevibacter ruminatium, Methanococcus mazei, and Methanosarcina sp. Methanogens comprise at least three major groups: Group I contains Methanobacterium and Methanobreviabacter, Group II contains Methanococcus, and Group III contains several general including Methanospirillum and Methanosacina.
At least three different types of cell wall are found among the methanogens. The most complex is that of Group I, which is rigid and composed chiefly of pseudomurein, a peptidoylycan similar to the murcin of eubacteria. Pseudomurein contains N-acetyl- talosaminuronic acid instead of N-acetylmuramic acid, and lacks D-amino acids. In appearance the wall resembles those of Gram- positive eubacteria. In Methanococcus, of Group II, the wall is flexible and composed chiefly of proteins with traces of glucosamine. Methanospirillum, of Group III has the most complex cell wall. It is flexible, composed of at least two layers : an inner, electron-dense of unknown chemistry and the outer one appearing like a membrane in cross section but composed entirely of protein. This protein is resistant to hydrolysis by proteinases (as trypsin) and to solubilisation by detergents as sodium dodecyl sulphate, SDS.
Methanogens contain several cofactors not found in other bacteria. Three of them (methanopterin, methanofuran, and CoM) are carriers of the C1 unit during its reduction from CO2 to CH4. Factor420 functions as hydrogen carrier and F430 is the prosthetic group of methyl-CoM reductase, the last enzyme in reduction pathway.
Methanogens are ubiquitous in highly reducing habitats (Eh <- 0.33V). The impact of methanogens on their environments is substantial.
[II] Halobacteriaceae (Halophiles)
The genera Halobacterium and Halococcus are included in this family and they have characteristics of archaebacteria. Light energy is converted to ATP by bacteriorhodopsin, a red pigment located in the purple membrane portion of the red membrane of this bacterium. Thus in addition to respiration, there is also light-dependent ATP generation.
Besides the above unique metabolic features, Halobacteriaceae are obligate halophiles, growing only in media of at least 15% NaCl concentration. Members are found in ecosystems that have extremely high NaCl concentrations, such as salt lakes, the Dead Sea, and salt-preserved foods.
Salt lakes occur in arid regions where evaporation exceeds freshwater inflow or where a lake is fed by a salt spring. Since high concentrations of salt dehydrate cells and denature enzymes, relatively few organisms can grow in highly saline waters. Very often the biota of salt lakes is restricted to a few halophiles (salt-requiring) and salt-tolerant bacteria. Halophiles have high internal concentrations of KCl and their enzymes must have greater tolerance of salt than those unable to tolerate salt. In many cases high salt concentrations are required by halophiles to maintain their enzymatic activities. Many halophiles have unusual membranes, such as the purple bilayer membranes of Halobacterium. The cell wall of this bacterium lacks murein and appears to be stabilised by sodium ions. The principal component of the cell wall is a large (MW = 200,000) acidic glycoprotein, other component being non-glycosylated protein and glycolipid. The cell wall of Halococcus is different and resembles that of Gram-positive eubacteria. The ribosomes of Halobacterium require high concentrations of potassium for stability. These are the adaptive features that are used by halophiles to live in saturated brine environments of salt lakes.
They are a heterogeneous group defined by their ability to grow at high temperature and low pH. Several subgroups have been identified: Sulfolobus, Thermoplasma and Thermoproteus group.
Sulfolobus is a facultative chemoautotroph found extensively all over the world in hot acid springs and soils. The cells are irregularly lobate spherical. Temperature optima for growth vary among isolates from 63° to 80° C; PH optima normally around 2.0. The range of conditions over which it grows is fairly wide temperature of 55° to 85° C, pH of 1 to 5.9. Although Sulfolobus can grow on organic compounds (perhaps fermentatively), in its natural habitats it probably grows as a respiratory chemoautotroph. Geothermal steam or hot water leaches much amounts of iron and sulphide, which is rapidly oxidised to elemental sulphur by oxygen or ferric ion, cither chemically or biologically. This bacterium rapidly oxidises H2S. The principal substrate in hot spring and may be also in hot soils, is elemental sulphur and it grows on the surface of droplets or crystals of sulphur oxidising it to H2SO4, responsible for the acidic habitats.
Thermoplasma is a facultative anaerobe that uses small number of mono and disaccharides as carbon and energy source. This microbe is found only in the refuse piles from coal mines which contain residual coal and substantial iron pyrite (FeS). Oxidation of FeS by chemoautotrophic bacteria acidifies and heats the piles, creating a favourable environment for Thermal plasma (pH 0.5 to 4.5; temp. 37o to 65° C). Small organic molecules in coal spoils (produced by pyrolysis of larger ones) are utilised by Thermoplasma. We still do not know the original habitat of this microbe, as attempts to isolate it from hot acidic springs or animal stomach have failed. Perhaps the true natural habitat is coal veins exposed to atmosphere by geological processes. Thermoplasma lacks a cell wall but cell membrane contains large amounts of lipopolysaccharide and glycoprotein, both of which contain mannose.
Thermoproteus group consists of thermoacidophiles whose metabolism is chiefly or exclusively respiratory with elemental sulphur serving as terminal electron acceptor. The product is H2S, which is a required nutrient for organisms in this group. They all are strict anaerobes. The only habitats that could yield these microbes are geothermal areas of Iceland, where they are widespread. Two genera of this group are, Thermoproteus and Desulfurococcus. Thermoproteus are long thin rods, with strictly respiratory metabolism, growing over a temperature range of 78° to 95°C, and a pH range of 2.5 to 6. Desulfurococcus are spherical cells, with fermentative as well as respiratory metabolism, and grow over a temperature range of 75° to 95°C and a pH range of 5 to 7.
Though these are not archaebacteria, they are being referred here due to the reason that they are a special ecological group found in extremely high temperature habitats. They are found in hot springs and thermal vents, the most extreme and extensive high-temperature habitats in areas of volcanic activity. Hot Springs have temperatures near 100°C. Microbes of these areas must be able to function at such high temperatures. The growth of microbes of hot springs is also limited by low organic matter, oxygen and depending on a particular hot spring, either acid or alkaline pH values. The water outflowing the hot spring, flows down channels, establishing a temperature gradient, with a clear zonation of microorganisms, occupying habitats of differing maximal temperatures along this temperature gradient; bacteria being most tolerant of extreme temperature. At temperatures above 75°C only a few bacterial species, as members of the genera Thermus appear to grow.
Bacillus stearothermophilus is dominant in hot springs in temperature zone of 55-70°C, but many other microbes as cyanobacteria and algae also occur there. Cyanobacteria occur as layers of growth within specific zones of thermal ponds. Cyanobacteria grow in higher temperatures zones than algae which are restricted to growth below 55°C.
Thermal vent communities are located at depths of 800-1000 m, where seawater percolates deeply into the crust to react with hot core materials. These regions receive no sunlight and there is minimal nutrient input from the water above. In these areas the community is supported energetically by the chemoautotrophic oxidation of reduced sulphur primarily by Beggiatoa, Thiomicrospira, and additional sulphide or sulphur oxidisers of great morphological diversity.
Many of the organisms of hot springs and thermal vents are obligate thermophiles and are restricted to growth at high temperatures. They have several adaptive features to carry out metabolism at temperatures of over 60o C. Many these microbes produce enzymes that are not readily denatured at high temperatures. Sometimes unusual amino acid sequences occur in their proteins, stabilising at high temperatures, Their membranes possess a major proportion of high molecular weight, and branched fatty acids that allow them to maintain semi-permeability at high temperatures. Thermophiles have high proportions of guanine and cytosine in DNA that raise the melting point and add stability to the DNA molecule.
Some eubacteria are acidophiles, restricted to growth at low pH values. Some members of the genus Thiobacillus are acidophilie, and grow only at pH values near 2.0. Thiobacillus thiooxidans has a minimum 1.0, optimum 20-28 and maximum 4.0-6.0 pH values. Acidophiles possess physiological adaptations that allow enzymatic and membrane transport activities at low pH. The cell membrane of such bacteria breaksdown and can not function at neutral pH value. (BSc Microbiology of Extreme Environments Notes Study Material)
Some species of Thiobacillus, oxidise only sulphur compounds, whereas others, as T. ferrooxidans, also oxidise ferrous to ferric iron for ATP generation (chemolithotrophs). Thiobacillus spp. can be used in the recovery of minerals, including uraniurf, and their oxidation of reduced iron and sulphur compounds mobilises various metals so that they can be extracted from even low-grade ores. T. thiooxidans used in biological metal recovery is acidophilic with optimum growth in the pH range of 1.0-3.5. The metabolic activities of this bacterium, found often in association with waste coal heaps, produce mine drainage, a serious ecological problem associated with some coal mining operations.
Acid mine drainage
Thiobacillus spp. is used in bioleaching processes for mineral recovery. Oxidation of elemental sulphur to sulphate leads to environmental accumulation of sulphuric acid. Acid mine drainage is the result of the metabolism of sulphur and iron-oxidising bacteria, which occur in hot sulphur springs and smouldering coal wastes-at high temperatures. Since there exist extreme acidic conditions also in such areas, the bacteria are acidophiles too. Hence the term thermoacidophiles is used for this group of bacteria. Coal in geological deposits is often associated with pyrite (FeS2) and when coal mining activities expose pyrite ores to atmospheric oxygen, the combination of auto-oxidation and microbial sulphur and iron oxidation produces large amounts of acid. The acid kills aquatic life and renders’ water unfit for drinking. Strip mining of coal recovery causes acid mine drainage. This method removes the overlying soil and rock, leaving porous rubble of tailings exposed to O2 and percolating water. Oxidation of reduced iron and sulphur in the tailings produces acidic products, causing the pH to drop rapidly. A strip-mined piece of land continues to produce acid mine drainage until most of the sulphide is oxidised and leached out; recovery of this land may take 50-150 years. (BSc Microbiology of Extreme Environments Notes Study Material)
The overall reaction of the oxidation of pyrite can be summarised as 2FeS2 + 7.5 O2 + 7H20 – 2Fe(OH)3 + 4H2SO4. The acid produced accounts for high acidity and the precipitated ferric hydroxide. The mechanism of pyrite oxidation in acid mine drainage is quite complex. At neutral pH, oxidation by atmospheric O2 occurs rapidly and spontaneously but below pH 4.5, auto-oxidation is slowed drastically. The stalked iron bacterium, Metallogenium in the pH range of 4.5-3.5 catalyses the oxidation of iron. As the pH drops below 3.5, the acidophilic bacteria (spp. of Thiobacillus) oxidise the reduced iron sulphide in the pyrite. The rate of microbial oxidation of FeS is several hundred times greater than the rate of spontaneous oxidation. Microbial oxidation of sulphur and iron is infact responsible for the continued production of high levels of acid mine drainage.
BSc Microbiology of Extreme Environments Notes Study Material