Published on January 25, 2008
EXTREMOPHILESNATURE’S ULTIMATE SURVIVORS: EXTREMOPHILES NATURE’S ULTIMATE SURVIVORS HOUSSEIN A. ZORKOT ROBERT WILLIAMS ALI AHMAD UNIVERSITY OF MICHIGAN-DEARBORN MICROBIOLOGY EXTREMOPHILES: EXTREMOPHILES What are they? Types of Extremophiles Extreme Prokaryotes Extreme Eukaryotes Extreme Viruses Evolution of Extremophiles Biotechnological Uses Industrial Uses Extraterrestrial Extremophiles? What are Extremophiles?: What are Extremophiles? Extremophiles are microorganisms— whether viruses, prokaryotes, or eukaryotes— that survive under harsh environmental conditions that can include atypical temperature, pH, salinity, pressure, nutrient, oxic, water, and radiation levels Types of Extremophiles: Types of Extremophiles Types of Extremophiles Types of Extremophiles: Types of Extremophiles Other types include: Barophiles -survive under high pressure levels, especially in deep sea vents Osmophiles –survive in high sugar environments Xerophiles -survive in hot deserts where water is scarce Anaerobes -survive in habitats lacking oxygen Microaerophiles -survive under low-oxygen conditions only Endoliths –dwell in rocks and caves Toxitolerants -organisms able to withstand high levels of damaging agents. For example, living in water saturated with benzene, or in the water-core of a nuclear reactor Environmental Requirements: Environmental Requirements Surviving the Extremes: Surviving the Extremes EXTREME PROKARYOTES Hyperthermophiles: EXTREME PROKARYOTES Hyperthermophiles -Members of domains Bacteria and Archaea -Held by many scientists to have been the earliest organisms -Early earth was excessively hot, so these organisms would have been able to survive Morphology of Hyperthermophiles: Morphology of Hyperthermophiles -Heat stable proteins that have more hydrophobic interiors, which prevents unfolding or denaturation at higher temperatures -Have chaperonin proteins that maintain folding -Monolayer membranes of dibiphytanyl tetraethers, consisting of saturated fatty acids which confer rigidity, preventing them from being degraded in high temperatures -Have a variety of DNA-preserving substances that reduce mutations and damage to nucleic acids, such as reverse DNA gyrase and Sac7d -They can live without sunlight or organic carbon as food, and instead survive on sulfur, hydrogen, and other materials that other organisms cannot metabolize The red on these rocks is produced by Sulfolobus solfataricus, near Naples, Italy Some Hyperthermophiles: Some Hyperthermophiles Thermus aquaticus 1m Pyrococcus abyssi 1m Frequent habitats include volcanic vents and hot springs, as in the image to the left Deep Sea Extremophiles: Deep Sea Extremophiles The deep-sea floor and hydrothermal vents involve the following conditions: low temperatures (2-3º C) – where only psychrophiles are present low nutrient levels – where only oligotrophs present high pressures – which increase at the rate of 1 atm for every 10 meters in depth (as we have learned, increased pressure leads to decreased enzyme-substrate binding) barotolerant microorganisms live at 1000-4000 meters barophilic microorganisms live at depths greater than 4000 meters A black smoker, a submarine hot spring, which can reach 518- 716°F (270-380°C) Extremophiles of Hydrothermal Vents: Extremophiles of Hydrothermal Vents A cross-section of a bacterium isolated from a vent. Often such bacteria are filled with viral particles which are abundant in hydrothermal vents A bacterial community from a deep-sea hydrothermal vent near the Azores Natural springs which vent warm or hot water on the sea floor near mid-ocean ridges. Associated with the spreading of the earth’s crust. High temperatures and pressures 0.2m 1m Psychrophiles: Psychrophiles Some microorganisms thrive in temperatures well below the freezing point of water, such as in Antarctica Some researchers believe that psychrophiles live in conditions mirroring those found on Mars Slide14: Psychrophiles possess: -proteins rich in -helices and polar groups which allow for greater flexibility -“antifreeze proteins” that maintain liquid intracellular conditions by lowering freezing points of other biomolecules -membranes that are more fluid, containing unsaturated cis-fatty acids which help to prevent freezing -active transport at lower temperatures Halophiles: Halophiles -Divided into mild (1-6%NaCl), moderate (6-15%NaCl), and extreme (15-30%NaCl) -Halophiles are mostly obligate aerobic archaea How do halophiles survive high salt concentrations? -by interacting more strongly with water such as using more negatively charged amino acids in key structures -by making many small proteins inside the cell, and these, then, compete for the water -and by accumulating high levels of salt in the cell in order to outweigh the salt outside Barophiles: Barophiles -Survive under levels of pressure that are otherwise lethal to other organisms -Usually found deep in the earth, in the deep sea, hydrothermal vents, etc -scientists believe that barophiles may be able to survive on the Moon and other places in space A sample of barophilic bacteria from the earth’s interior 1m Xerophiles: Xerophiles Extremophiles which live in water-scarce habitats, such as deserts Produce desert varnish as seen in the image to the left Desert varnish is a thin coating of Mn, Fe, and clay on the surface of desert rocks, formed by colonies of bacteria living on the rock surface for thousands of years SOME COMMON GENERA OF PROKARYOTE EXTREMOPHILES: SOME COMMON GENERA OF PROKARYOTE EXTREMOPHILES Thermotoga Aquifex Halobacterium Methanosarcina Thermoplasma Thermococcus Thermoproteus Pyrodictium Ignicoccus 2um 1.8um 1um 0.6um 0.9um 0.9um 1.3um 0.6um 0.7um Deinococcus radioduransThe Radiation Resistor: Deinococcus radiodurans The Radiation Resistor -Possesses extreme resistance to up to 4 million rad of radiation, genotoxic chemicals (those that harm DNA), oxidative damage from peroxides/superoxides, high levels of ionizing and ultraviolet radiation, and dehydration -It has from four to ten DNA molecules compared to only one for most other bacteria -Contains many DNA repair enzymes, such as RecA, which matches the shattered pieces of DNA and splices them back together. During these repairs, cell-building activities are shut off and the broken DNA pieces are kept in place 0.8m Chroococcidiopsis The Cosmopolitan Extremophile: Chroococcidiopsis The Cosmopolitan Extremophile -A cyanobacteria which can survive in a variety of harsh environments, such as hot springs, hypersaline habitats, hot, arid deserts throughout the world, and in the frigid Ross Desert in Antarctica -Possesses a variety of enzymes which assist in such adaptation 1.5m Other Prokaryotic Extremophiles: Other Prokaryotic Extremophiles Gallionella ferrugineaand (iron bacteria), from a cave Anaerobic bacteria 1m 1m Current efforts in microbial taxonomy are isolating more and more previously undiscovered extremophile species, in places where life was least expected EXTREME EUKARYOTESTHERMOPHILES/ACIDOPHILES: EXTREME EUKARYOTES THERMOPHILES/ACIDOPHILES 2m EXTREME EUKARYOTESPSYCHROPHILES: EXTREME EUKARYOTES PSYCHROPHILES Snow Algae (Chlamydomonas nivalis) A bloom of Chloromonas rubroleosa in Antarctica These algae have successfully adapted to their harsh environment through the development of a number of adaptive features which include pigments to protect against high light, polyols (sugar alcohols, e.g. glycerine), sugars and lipids (oils), mucilage sheaths, motile stages and spore formation 2m EXTREME EUKARYOTESENDOLITHS: EXTREME EUKARYOTES ENDOLITHS Quartzite from Johnson Canyon, California. Sample shows green bands of endolithic algae. Rock is 9.5 cm wide -Endoliths (also called hypoliths) are usually algae, but can also be prokaryotic cyanobacteria, that exist within rocks and caves -Often are exposed to anoxic (no oxygen) and anhydric (no water) environments EXTREME EUKARYOTESPARASITES: EXTREME EUKARYOTES PARASITES -Members of the Phylum Protozoa, which are regarded as the earliest eukaryotes to evolve, are mostly parasites -Parasitism is often a stressful relationship on both host and parasite, so they are considered extremophiles Trypanosoma gambiense, causes African sleeping sickness Balantidium coli, causes dysentery-like symptoms 15m 20m EXTREME VIRUSES: EXTREME VIRUSES Virus-like particles isolated from the extreme environment of Yellowstone National Park hot springs Viruses are currently being isolated from habitats where temperatures exceed 200°F Instead of the usual icosahedral or rod-shaped capsids that known viruses possess, researchers have found viruses with novel propeller-like structures These extreme viruses often live in hyperthermophile prokaryotes such as Sulfolobus 40nm Phylogenetic Relationships: Phylogenetic Relationships Extremophiles are present among Bacteria, form the majority of Archaea, and also a few among the Eukarya CLASSIFICATION OF EXTREMOPHILES Slide28: -Members of Domain Bacteria (such as Aquifex and Thermotoga) that are closer to the root of the “tree of life” tend to be hyperthermophilic extremophiles -The Domain Archaea contain a multitude of extremophilic species: Phylum Euryarchaeota-consists of methanogens and extreme halophiles Phylum Crenarchaeota-consists of thermoacidophiles, which are extremophiles that live in hot, sulfur-rich, and acidic solfatara springs Phylum Korarchaeota-new phylum of yet uncultured archaea near the root of the Archaea branch, all are hyperthermophiles -Most extremophilic members of the Domain Eukarya are red and green algae PHYLOGENETIC RELATIONSHIPS Chronology of Life: Chronology of Life The First Organisms?: The First Organisms? Early Earth was largely inhospitable: high CO2/H2S/H2 etc, low oxygen, and high temperatures Lifeforms that could evolve in such an environment needed to adapt to these extreme conditions H2 was present in abundance in the early atmosphere. Many hyperthermophiles and archaea are H2 oxidizers Thus, it is widely held that extremophiles represent the earliest forms of life with non-extreme forms evolving after cyanobacteria had accumulated enough O2 in the atmosphere Results of rRNA and other molecular techniques have placed hyperthermophilic bacteria and archaea at the roots of the phylogenetic tree of life Evolutionary Theories: Evolutionary Theories Consortia- symbiotic relationships between microorganisms, allows more than one species to exist in extreme habitats because one species provides nutrients to the others and vice versa Genetic drift appears to have played a major role in how extremophiles evolved, with allele frequencies randomly changing in a microbial population. So alleles that conferred adaptation to harsh habitats increased in the population, giving rise to extremophile populations Geographic isolation may also be a significant factor in extremophile evolution. Microorganisms that became isolated in more extreme areas may have evolved biochemical and morphological characteristics which enhanced survival as opposed to their relatives in more temperate areas. This involves genetic drift as well Slower Evolution: Slower Evolution -Extremophiles, especially hyperthermophiles, possess slow “evolutionary clocks” -That is, they have not evolved much from their ancestors as compared to other organisms -Hence, hyperthermophiles today are similar to hyperthermophiles of over 3 billion years ago -Slower evolution may be the direct result of living in extreme habitats and little competition -By contrast, other extremophiles, such as extreme halophiles and psychrophiles, appear to have undergone faster modes of evolution since they live in more specialized habitats that are not representative of early earth conditions Mat Consortia: Mat Consortia -Microbial mats consist of an upper layer of photosynthetic bacteria, with a lower layer of nonphotosynthetic bacteria -These consortia may explain some of the evolution that has taken place: extremophiles may have relied on other extremophiles and non-extremophiles for nutrients and shelter -Hence, evolution could have been cooperative A mat consortia in Yellowstone Mat Consortia Slide34: USES OF EXTREMOPHILES HYPERTHERMOPHILES (SOURCE) USES DNA polymerases DNA amplification by PCR Alkaline phosphatase Diagnostics Proteases and lipases Dairy products Lipases, pullulanases and proteases Detergents Proteases Baking and brewing and amino acid production from keratin Amylases, a-glucosidase, pullulanase and xylose/glucose isomerases Baking and brewing and amino acid production from keratin Alcohol dehydrogenase Chemical synthesis Xylanases Paper bleaching Lenthionin Pharmaceutical S-layer proteins and lipids Molecular sieves Oil degrading microorganisms Surfactants for oil recovery Sulfur oxidizing microorganisms Bioleaching, coal & waste gas desulfurization Hyperthermophilic consortia Waste treatment and methane production USES OF EXTREMOPHILES: USES OF EXTREMOPHILES PSYCHROPHILES (SOURCE) USES Alkaline phosphatase Molecular biology Proteases, lipases, cellulases and amylases Detergents Lipases and proteases Cheese manufacture and dairy production Proteases Contact-lens cleaning solutions, meat tenderizing Polyunsaturated fatty acids Food additives, dietary supplements Various enzymes Modifying flavors b-galactosidase Lactose hydrolysis in milk products Ice nucleating proteins Artificial snow, ice cream, other freezing applications in the food industry Ice minus microorganisms Frost protectants for sensitive plants Various enzymes (e.g. dehydrogenases) Biotransformations Various enzymes (e.g. oxidases)Bioremediation, environmental biosensors Methanogens Methane production USES OF EXTREMOPHILES: USES OF EXTREMOPHILES HALOPHILES (SOURCE) USES Bacteriorhodopsin Optical switches and photocurrent generators in bioelectronics Polyhydroxyalkanoates Medical plastics Rheological polymers Oil recovery Eukaryotic homologues (e.g. myc oncogene product) Cancer detection, screening anti-tumor drugs Lipids Liposomes for drug delivery and cosmetic packaging Lipids Heating oil Compatible solutes Protein and cell protectants in variety of industrial uses, e.g. freezing, heating Various enzymes, e.g. nucleases, amylases, proteases Various industrial uses, e.g. flavoring agents g-linoleic acid, b-carotene and cell extracts, e.g. Spirulina and Dunaliella Health foods, dietary supplements, food coloring and feedstock Microorganisms Fermenting fish sauces and modifying food textures and flavors Microorganisms Waste transformation and degradation, e.g. hypersaline waste brines contaminated with a wide range of organics Membranes Surfactants for pharmaceuticals USES OF EXTREMOPHILES: USES OF EXTREMOPHILES ALKALIPHILES (SOURCE) USES Proteases, cellulases, xylanases, lipases and pullulanases Detergents Proteases Gelatin removal on X-ray film Elastases, keritinases Hide dehairing Cyclodextrins Foodstuffs, chemicals and pharmaceuticals Xylanases and proteases Pulp bleaching Pectinases Fine papers, waste treatment and degumming Alkaliphilic halophiles Oil recovery Various microorganisms Antibiotics ACIDOPHILES (SOURCE) USES Sulfur oxidizing microorganisms Recovery of metals and desulfurication of coal Microorganisms Organic acids and solvents Taq Polymerase: Taq Polymerase Isolated from the hyperthermophile Thermus aquaticus Much more heat stable Used as the DNA polymerase in the very useful Polymerase Chain Reaction (PCR) technique which amplifies DNA samples Alcohol Dehydrogenase: Alcohol Dehydrogenase -Alcohol dehydrogenase (ADH), is derived from a member of the archaea called Sulfolobus solfataricus -It works under some of nature's harshest volcanic conditions: It can survive to 88°C (190ºF) - nearly boiling - and corrosive acid conditions (pH=3.5) approaching the sulfuric acid found in a car battery (pH=2) -ADH catalyzes the conversion of alcohols and has considerable potential for biotechnology applications due to its stability under these extreme conditions Bacteriorhodopsin: Bacteriorhodopsin -Bacteriorhodopsin is a trans-membrane protein found in the cellular membrane of Halobacterium salinarium, which functions as a light-driven proton pump -Can be used for electrical generation Bioremediation: Bioremediation Bioremediation is the branch of biotechnology that uses biological processes to overcome environmental problems Bioremediation is often used to degrade xenobiotics introduced into the environment through human error or negligence - Part of the cleanup effort after the 1989 Exxon Valdez oil spill included microorganisms induced to grow via nitrogen enrichment of the contaminated soil Bioremediation: Bioremediation Slide43: Psychrophiles as Bioremediators Bioremediation applications with cold-adapted enzymes are being considered for the degradation of diesel oil and polychlorinated biphenyls (PCBs) - Health effects that have been associated with exposure to PCBs include acne-like skin conditions in adults and neurobehavioral and immunological changes in children. PCBs are known to cause cancer in animals An End to Pollution?: An End to Pollution? New and innovative methods are being developed that utilize extremophiles for the elimination of pollution resulting from oil slicks, toxic chemical spills, derelict mines, etc Life in Outer Space?: Life in Outer Space? -Scientists have decided on 3 requirements for life: water energy carbon -Astrobiology: field of biology dealing with the existence of life beyond earth -Astrobiologists are currently looking for life on Mars, Jupiter’s moon Europa, and Saturn’s moon Titan -Such life is believed to consist of extremophiles that can withstand the cold and pressure differences -Mudslide-like formations have been found on Mars (left). These appear to have been caused by water movements. Psychrophiles may exist there Image courtesy of the Current Science & Technology Center Life in Outer Space?: Life in Outer Space? -Europa is thought to have an ice crust shielding a 30-mile deep ocean. Reddish cracks (left) are visible in the ice and may be evidence of living populations -Titan is enveloped with a hazy gas (left) that is believed to contain some organic molecules, ie methane. This may provide sustenance for life on Titan’s surface Images courtesy of the Current Science & Technology Center Life in Outer Space?: Life in Outer Space? -Scientists have found that meteorites contain amino acids and simple sugars, very important building blocks. These may serve to spread life throughout the universe Image courtesy of the Current Science & Technology Center -A sample of stratospheric air had shown a myriad of bacterial diversity 41 km above the earth’s surface (Lloyd, Harris, & Narlikar, 2001) Indeed, we may not be alone CONCLUSIONS: CONCLUSIONS -Extremophiles are a very important and integral part of the earth’s biodiversity They: - reveal much about the earth’s history and origins of life - possess amazing capabilities to survive in the extremes - are proving to be beneficial to both humans and the environment -may exist beyond earth Questions?: Questions?