- xerophiles => anhydrobiosis : Artemia salina, nematodes, microbes, fungi, lichens. It may cause irreversible phase changes to lipids, protein and nucleic acids such as denaturation, structural breakage through Maillard reactions and accumulation of R.O.S. during drying. Xeropholous habitats are only tolerated by the Fungi.
- photosynthesis or phototrophism : sunlight energy in (eu)photic zone (uppermost layer of a body of water or soil that receives enough sunlight to permit the occurrence of photosynthesis : a chemical combination caused by the action of light; specifically the formation of carbohydrates (with release of molecular oxygen) from carbon dioxide and water in the chlorophyll tissue of plants and blue-green algae under the influence of light. In bacteria, photosynthesis employs hydrogen sulfide, molecular hydrogen, and other reduced compounds in place of water, so that molecular oxygen is not released. The general reaction is : 6CO2 + 12H2A + n hu => C6H12O6 + 12A + 6H2O.
- Blinks effects : brief enhancement in photosynthesis which follows shifts from a long wavelength to a shorter wavelength
- Emerson effect : the photosynthetic efficiency of a long wavelength of light is enhanced by simultaneous exposure of plant cells to shorter wavelengths of light.
- an inorganic compound (photolithotroph)
- oxygenic photosynthesis (Cyanobacteria, Algae, Plantae). Clorophyll (lA max= 680 and 780 nm).
- 6CO2 + 12H2O + n hu => C6H12O6 + 6O2 + 6H2O
- anoxygenic photosynthesis (properly said photosynthetic Bacteria, no Eukarya).
- green sulfur Bacteria (Chlorobiaceae). Bacteriochlorophyll (lA max = 700-900 nm) and bacteriopheophitin (BPh)
- 6CO2 + 12H2S + n hu => C6H12O6 + 6S2 + 6H2O
- green non sulfur Bacteria (Chloroflexaceae)
- purple sulfur Bacteria (Chromatiaceae and Ectothiorhodospiraceae). Bacteriochlorophyll (l = 700-900 nm) and bacteriopheophitin (BPh)
- 6CO2 + 12HSO3- + n hu => C6H12O6 + 12HSO4- + 6H2O
- 6CO2 + 12 thiosulphate + n hu => C6H12O6 + ? + 6H2O
- purple non sulfur Bacteria (Rhodospirillaceae)
- 6CO2 + 12 H2 + n hu => C6H12O6 + 6H2O
- an organic compound (photoorganotroph)
- anoxygenic photosynthesis (properly said photosynthetic Bacteria, no Eukarya).
- purple non sulfur Bacteria (Rhodospirillaceae)
- 6CO2 + 12 lactate + n hu => C6H12O6 + 12 Pyr + 6H2O
- 6CO2 + 12 isopropanol + n hu => C6H12O6 + 12 acetone + 6H2O
- cyclic
- non cyclic
- chemosynthesis : the synthesis of carbohydrate from carbon dioxide and water as a result of the energy derived from chemical reactions (chemical bond energy passed to NADH through electron transfer), rather than from absorbed light. Such synthesis is carried out by certain bacteria and algae
- chemolithotrophic (organisms that oxidize unorganic compounds)
- NH4+ oxidizing : 2NH4+ + 3O2 = 2NO2- + 2H2O + 4H+ (e.g. : Nitrosomonas)
- NO2- oxidizing : 2NO2 + O2 = 2NO3- (e.g. : Nitrobacter)
- H2 oxidizing => H2O (?). Hydrogen-oxidizing bacterium : facultative lithotrophs that, in the absence of an oxidizable organic source, oxidize H2 for energy and synthesize carbohydrates with CO2 as their source of carbon.
- methanotroph : organism capable of oxidizing CH4
- chemoorganotrophic (organisms that oxidize organic compounds)
- carbohydrate oxidizing
- glucose oxidizing
- Embden-Meyerhof-Parnas (EMP) pathway or glycolysis
- aerobic glycolysis : when occurs in a cell capable of aerobic respiration
- anaerobic glycolysis : when occurs in a cell not capable of aerobic respiration (i.e. capable of anaerobic respiration or of fermentation)
- Warburg-Dickens-Horecker or pentose phosphate pathway
- Entner-Doudoroff pathway
- carboxylic acid oxidizing
- amino acid oxidizing (rare)
- protein oxidizing
- ... respiration (requires cytochromes), in which the final acceptor may be ..
- O2 (aerobic respiration) => H2O
- another oxigenated inorganic compound (anaerobic respiration)
- NO3- (see above) => NH3
- SO4- (see below) => -SH
- HCO3- => (as in acetic fermentation)
- ... fermentation : a kind of energy production (the definition also includes the oxidizing reactions above debscribed !) that doesn't require cytochromes and don't change the global oxidation status of the substrate. Organic compounds serve as both electron donors and electron acceptors. Fermentations are classified according to the ultimate product :
- acetic fermentation (e.g. : in Acetobacter)
- 2,3-butanediolic fermentation (e.g. : in Pseudomonas spp.and Enterobacter spp.)
- butyl alcohol fermentation (e.g. in Clostridium spp.)
- butyric fermentation (e.g. : in Clostridium spp.)
- citric fermentation (e.g. : in Aspergillus spp.)
- ethanolic (alcoholic) fermentation (e.g. : in Saccharomyces spp.)
- formic fermentation (e.g. in Enterobacter spp.)
- isopropyl alcohol fermentation (e.g. in Clostridium spp.)
- lactic fermentation (e.g. : in Lactobacillus spp., metazoan cells)
- propionic fermentation (e.g. in Propionibacterium spp.)
- succinic fermentation (byproduct of alcoholic fermentation)
- geothermosynthetic (geothermic energy in deep seas; found in bacterial species at hydrothermal vents)
- H2S + Q =>
- H2 + Q =>
- Osedax frankpressi, found in a whale fall in the trough of Monterey Canyon, some 3,000 metres deep, consist of a balloon-like egg sac, which branches into a greenish root system growing into the whalebone to extract fats and oils from the marrow. Symbiotic bacteria that live inside the roots break down the lipids, but how nutrients are transferred from the bones to the bacteria and then to the worms is not yet known. The 2 new species diverged about 42 million years ago, which is about the same time that whales first evolved. Whereas female worms are several inches in length, males are little more than microscopic threads, which seem to act as nothing more than sperm factories. A female worm can sweep up to 100 males at once into her egg sac, where fertilization occurs. Goffredi speculates that the sex a larva develops into is determined when it is floating around in the water searching for something to land on. If the larva encounters a clear patch of whalebone, it becomes a female. But if there is no place for the larva to land except on another female, it does the next best thing and becomes a male, to provide that female with sperm.
Web resources :
Diauxia : some substrates are metabolized by constitutive enzyme and inhibit the expression of the inducible enzymes needed to metabolize other substrates. Only when the preferred substrate(s) is completely consumed inhibition is removed and the cell is able to synthetize such enzymes.
- aerobes or oxybionts (with transport system (including cyt c) for O2 reduction and ROS detoxification systems (i.e. : catalase, SOD, peroxidases, ...). Biochemical oxygen demand (BOD) : amount of dissolved oxygen consumed in five days by biological processes breaking down organic matter.
- strictly aerobes : only capable of aerobic respiration (e.g. : Mycobacteria, Homo sapiens)
- facultative aerobes : better growth in oxigenated environments (e.g. : Enterobacteriacee)
- microaerophilus or microaerobes : maximal growth at [O2]rel = 5% (i.e. PO2 < 0.2 atm), [CO2]rel = 10% and [N2]rel = 85%. (e.g. : Campylobacter, Helicobacter)
- anaerobes or anoxybionts (with no transport system for O2 reduction (i.e. no cyt c), so capable only of anaerobic glycolysis followed by anaerobic fermentation and/or fermentation : some Eukarya lack mitochondria and acquire hydrogenosome)
- aerotolerant or facultative anaerobes : they produce SOD and so can grow at [O2]rel < 8% (e.g. : Lactobacillus, Streptococcus, Clostridium)
- strictly or obligate anaerobes : inhibited at [O2]rel > 0.5% (i.e. PO2 > 10-2 atm) (e.g. Bacteroides fragilis, Peptostreptococcus magnus, Methanobacteria, Methanococci). Many species don't produce neither SOD nor catalase. [O2]rel = 0%, [CO2]rel = 10%, [H2]rel = 10% and [N2]rel = 85%.
- extremely O2 sensitive (EOS) : inhibited even by just some ppm of O2 !
- CO2-philes : Cyanidium caldarium grows in media ventilated with pure CO2
- carbon sources :
- autotrophs or holophytic (use CO2 : please note they must use another energy source because CO2 is not oxidizable in biological systems : e.g. photoautotrophs, chemoautotrophs). They (Algae, Plantae and some Bacteria) are primaryproducers : organisms that add biomass to the ecosystem by synthesizing organic molecules from CO2 and simple inorganic nutrients.
- methanogenic : CH3COOH à CH4 + CO2 (Methanobacteria)
- heterotrophs or holozooic (use a carbon compound more reduced than CO2 , although many can also use CO2 : please note the carbon source may also be at the same time even an energy source !). Organisms can also be classified on the basis of their main carbon source (auxanograms). E.g. most Bacteria, Fungi, Protozoa, Metazoa.
- Feeding ways
- saprozooic feeding : simple diffusion of metabolites along osmotic gradients.
- phagotrophic : form of feeding where animals engulf particulate nutrients, such as bacterial cells or detritus (detritivores)
- Feedings and environment
- parasitic
- necrotrophic : nutritional mechanism by which an organism produces a battery of hydrolytic enzymes to kill and break down host cells and then absorb nutritional compounds from the dead organic matter
- saprophyte : nonparasitic nutritional mechanism by which an organism obtains its food exclusively from the degradation of nonliving organic material
- nitrogen metabolism :
- associative dinitrogen fixation : close interaction between a free-living diazotrophic organism and a higher plant that results in an enhanced rate of dinitrogen fixation.
- dinitrogen-fixing Bacteria (ammonification by diazotroph) : N2 + 8e- + 8H+ + 16ATP + 16H2O ==nitrogenase==> 2NH3 + H2 + 16ADP + 16Pi + 16H+ (e.g. nif+ Klebsiella pneumoniae strains, Pseudomonas aeruginosa, Azotobacter, Rhizobium, Cyanobacteria ...)
- nitrification : biological oxidation of NH4+ to NO2- and NO3-, or a biologically induced increase in the oxidation state of nitrogen. It consists of 2 reactions :
- NH4+ oxidizing : 2NH4+ + 3O2 = 2NO2- + 2H2O + 4H+ (e.g. : Nitrosomonas)
- NO2- oxidizing : 2NO2 + O2 = 2NO3- (e.g. : Nitrobacter)
- nitrate reduction : process whereby NO3- is reduced ...
- ... to NH4+ (ammonification) for amino acid and protein synthesis by plants and microorganisms (NO3- assimilation or assimilatory NO3- reduction)
- ... to various lower oxidation states (N2, N2O, NO) by denitrifying Bacteria (denitrification) using NO3- as the terminal electron acceptor in anaerobic respiration (dissimilatory NO3- reduction to NH4+ (DNRA)or), resulting in the reduction of NO3- to NH4+. It consists of ..
- NO3- reducing Bacteria : the major part of Bacteria
- NO3- + NADH + H+ ==nitrate reductase A==> NO2- + NAD+ + H2O
- NO2- reducing Bacteria
-
NO2- ==nitrate reductase B=> 2 NH3/NH4+
==?=> N
2 O ==> N2
Usenet bionet.biology.n2-fixation
heterotrophic nitrification : biochemical oxidation of NH4+ to NO2- and NO3- by heterotrophic microorganisms.
- second-line elements
- Ca
- Cl
- Mg : e.g. cofactor in AlkP, PI-3,4,5-P3 3-phosphatase, a-galactosidase, ...
- P
- K
- Na
- S
- sulfur-fixing Bacteria : Thiobacillus thiooxidans (S2 => SO4-)
- sulphate reducing Bacteria : sulphate reductase
- sulphate non-reducing Bacteria :
- third-line elements (in all organisms)
- Co : e.g. cofactor in ribonucleoside triphosphate reductase and many other hydrolases
- Cu : e.g. cofactor in cyt c oxidase, nitrite reductase, SOD, ...
- Fe : e.g. in hemoproteins
- Mn : e.g. cofactor in catalase, SOD, Met-S-methyltransferase, arginase, pyruvate carboxylase, ...
- Zn : e.g. cofactor in alcohol dehydrogenase, dihydroorotate dehydrogenase, SOD, Met-S-methyltransferase, AlkP, PL-C, pyruvate carboxylase and many peptidases.
- fourth-line elements (only in some organisms)
- Al
- As
- B
- Br
- Cr
- F
- Ga
- I : e.g. in iodotyronines
- Mo : e.g. cofactor in xanthine dehydrogenase, aldehyde oxidase, nitrate reductases and nitrogenases (iron-molibdenum is a cofactor in xanthine oxidase and carbon monoxide oxygenase)
- Ni : e.g. cofactor in carbon-monoxide dehydrogenase and urease
- Se : e.g. SeCys (encoded by the opal (UGA) stop codon !) in Escherichia coli formate dehydrogenase and mammalian (at least human and murine) glutathione peroxidase.
- Si
- W : e.g. cofactor in formate dehydrogenase and carboxylate reductase
- V : e.g. cofactor in Azotobacter nitrogenase
- Cd : e.g. cofactor in b-Ala-His dipeptidase
- psychrophiles (<15 °C, optimum 5-10 °C) : e.g. Psychrobacter, Heteromita globosa, Chlamydomonas rivalis, Chloromonas (Scotiella), Ankistrodesmus, Raphionema, Mycanthococcus, some insects. Microbial communities and Himalayan midge are active at -18 °C. The only organism for which body water freezing is not lethal is the nematode Panagrolaimus davidi. Freezing avoidance and protection from damage during thawing are both ensured by antifreeze molecules that allow histeresis to occur, lowering the freezing point of water by 9-18°C : they are evolutionarily convergent, with that of the Antartic nonothenioid fish evolving from a pancreatic trypsinogen-like protease. Protein flexibility and conformational complimentarity must be enhanced because low levels of free energy tend to increase activation energies. Hypobiosis or "hibernation" : the state of having greatly reduced to no metabolism due to T-dependent decrease in chemical reactions rate. A strange ecosystem has been discovered beneath the Antarctic ice sheet. But the collapse of the ice shelf that allowed researchers to find it also threatens the community's future. The Larsen ice shelf is on the Antarctic Peninsula, the northern tip of the continent, which reaches up towards South America. Possibly as a result of global warming, a 3,250-square-kilometre piece of ice, roughly the size of Long Island or Cornwall, broke away from the peninsula in 2002. In March 2005, researchers from the US Antarctic Program were surveying a patch of sea bed that used to be covered by this ice. The area lies 850 metres below the waves and 100 kilometres from where the tip of the ice shelf once started. The researchers took video and still images of the ocean floor using a submerged sled towed behind their boat. They weren't expecting, or looking for, signs of life, but they found it. The pictures show a thick white mat covering the sea bed that resembles 'bacterial mats' seen in other unusual deep-sea communities and has gas bubbles rising from it. The video shows 'mud volcanoes' with large collections of clams clustered around them. The site is an example of a cold seep: a deep-sea site where sulphur-rich waters and natural gas leak from the ocean floor. Mud volcanoes form where the waters well up. Thick mats of bacteria thrive on the gas and sulphur, using chemosynthesis to manufacture organic compounds. Similar communities exist at underwater hydrothermal vents, where sulphur-rich waters are volcanically superheated. The discovery is significant because no seeps have been found at such a latitude before. It may be that there are many more such sites beneath the vast areas of sea covered by ice sheets. "The area beneath ice shelves is large and very, very poorly known. The discovery could be the missing piece of a puzzle that has stumped scientists studying cold seeps and other chemosynthetic systems. Sites in different oceans often host the same species, but it has not been clear how the fauna could travel the thousands of miles between the very specialized habitats they need. The Southern Ocean forms a natural gateway between all the other oceans. If more seeps occurred in the Southern Ocean it could be acting as a dispersal route to sites in other seas. But the surprising ecosystem's days could be numbered. The overlying ice shelf sheltered the site from physical disturbance and the organic debris that usually supports bottom-dwelling organisms. Now sediment and rocks are building up, and more usual Antarctic species are moving in. It could be a decade or less before the sites are buried. The bacterial mats show definite signs of decline, as species move in to feed on the accumulating organic matter and discover a tasty food source. If predators of these grazers follow, then the clams and many other species unique to the site could start to disappearref.
- psychrotrophs : Serratia, Yersinia, Listeria
- mesophiles (15-60 °C, optimum 37 °C) : e.g. Neisseria, Homo sapiens
- thermophiles (60-80 °C, optimum 50-65 °C) : e.g. Synechococcus lividis (Bacteria). The upper limit for Eukarya is ~ 60÷70°C and is reachable only by some Protozoa and Algae (Cyanidium caldarium) : Fungi resist up to 60°C (Alvinella pompejana), mosses up to 50°C, vascular plants up to 48°C, fish up to 40°C. These limits are due to :
- decrease in solubility of gases in water
- denaturation of protein and nucleic acids (100°C)
- degradation of chlorophyll (> 75°C)
- Voyage to the Deep (a University of Delaware site)
- Woods Hole Oceanographic Institution (WHOI)
- hypertermophiles (>80 °C) : only Prokarya, as they contain reverse gyrase which induces positive super-coiling of DNA which enhances its thermal stability. Pyrococcus at > 100°C. Pyrolobus fumarii lives at 113°C; an Fe(III)-using bacteerial strain from a hydrothermal vent of the Northeast Pacific Ocean grows at 121°C; the most resistant enzyme is amylopullulanase (142°C).
The towering limestone chimneys of Lost City, a unique field of hydrothermal vents deep beneath the Atlantic Ocean, are packed with unusual life forms. 5 years ago, a team of US and Swiss researchers stumbled upon this system of seafloor geysers while studying an underwater mountain. The team had time for only one five-hour dive in Alvin, a deep submersible vehicle the size of a small truck. But the researchers returned in 2003 to investigate the links between the geology, fluid chemistry and biology of these vents. In the last 30 years, > 200 vent fields have been discovered. Many lie along mid-ocean ridges where hot magma seeps through the Earth's crust, reacting with sea water to create a hot, acidic, sulphide-rich environment. Minerals in this water harden into black-smoker chimneys, whose emissions sustain diverse microbes, which in turn provide food for a thriving community of tubeworms, clams and shrimp. But Lost City is different. It lies about 15 km away from the Mid-Atlantic Ridge, near the top of the Atlantis massif, a mountain that is > 4,000 m tall. Sea water trickling deep into the massif reacts with mantle rock that is 1.5 million years old. The reaction releases heat and dissolves some of the minerals in the rock to form warm, alkaline water that rises from fractures in the sea floor. The water can reach 90°C and pH 11. When it meets cooler sea water, calcium carbonate precipitates, which gradually builds up the chalky chimneys. The inside walls of these porous spires house a colony of archaea that have adapted to a diet of hydrogen and methane, which also rise from the vent beneath. The whole system seems geared toward methane production or methane consumption," he says, which is "the kind of system that might have been present on the early Earth. A diverse range of life feeds on these primitive archaea at Lost City. But whereas the hallmark of the black-smoker systems are tubeworms well > 1 m long, most of the fauna of the Lost City vents, including nematodes and bivalves, are transparent and < 1 cm. This makes the vent landscape look relatively barren
Web resources :
- vacuum-tolerant : e.g. : microbes, insects, tardigrades, plant seeds.
- barophiles or piezophilic (up to 80 MPa in Mariana trench (10,898 meters under sea level); up to 100 MPa in the Challenger Deep in the West Pacific; > 600 MPa for tardigrades in perfluorocarbon). High pressure decreases membrane fluidity, that can be increased by using unsaturated fatty acids in membranes. Increased pressure can increase the optimal temperature (water boils at 100°C under 101 kPa at sea level, but some degrees above under major pressures) for microbial growth. Increasing pressure causes acidification of the central vacuole in the yeast Saccharomyces cerevisiae at about 40 MPa. Foraminifera live in mud at the bottom of Challenger Deep in the Mariana Trench, almost 11 km beneath the waves of the western Pacific Ocean. The pressure at this depth is a crushing 1,090 times that at the surface. Samples of sediment were collected from the trench using the Kaiko submarine. This remote-controlled deep-sea vessel made its first trip to the Mariana Trench in 1995; it was lost at sea on a mission in May 2003. From the samples, Kitazato's team recovered numerous bacteria and 432 living foraminifera. The latter measure a few dozen mm across; hundreds could crowd on to a pinhead. Most of the foraminifera were soft-walled, either spherical or needle-shaped, and coloured brown. Foraminifera are perhaps the most abundant ocean life after bacteria ; most have intricate shells made of calcium carbonate. But these shells are absent from the foraminifera found in Challenger Deep. Instead, 85% of the researchers' haul belongs to a soft-walled group called allogromiids, which make up only 5-20% of other foraminiferan communities nearer the surface. This is probably because the deepest ocean has little calcium carbonate, meaning that microbes may not be able to build a shell. As you go deeper and deeper you get to a depth called the calcium compensation point : below that you tend to get soft-walled foraminifera. Kitazato's group speculates that soft foraminifera thrive in the Mariana mud because they are among the few creatures that can withstand the huge pressures there. Geologists think that the trench was created over the past 6 million to 9 million years, during which time the ecosystem's less hardy species may literally have been crushed to death.
Chemical analyses of the pore waters from hundreds of deep ocean sediment cores have over decades provided evidence for ongoing processes that require biological catalysis by prokaryotes. This sub-seafloor activity of microorganisms may influence the surface Earth by changing the chemistry of the ocean and by triggering the emission of methane, with consequences for the marine carbon cycle and even the global climate. Despite the fact that only about 1% of the total marine primary production of organic carbon is available for deep-sea microorganisms, sub-seafloor sediments harbour over half of all prokaryotic cells on Earth. This estimation has been calculated from numerous microscopic cell counts in sediment cores of the Ocean Drilling Program. Because these counts cannot differentiate between dead and alive cells, the population size of living microorganisms is unknown. Using ribosomal RNA as a target for the technique known as catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH), they provide direct quantification of live cells as defined by the presence of ribosomes. A large fraction of the sub-seafloor prokaryotes is alive, even in very old (16 million yr) and deep (> 400 m) sediments. All detectable living cells belong to the Bacteria and have turnover times of 0.25–22 yr, comparable to surface sedimentsref. Sediments that lie hundreds of metres below the ocean floor contain living bacteria, an analysis has shown. And according to the study these microbes could produce significant amounts of methane, a gas implicated in global warming. Marine sediments cover about 70% of the Earth and harbour more than half of the microorganisms on the planet. Unable to discriminate between living and dead cells in the deep ocean floor, scientists have long debated how much of its biological content is active. To solve this riddle, a team of researchers set out in 2001 to take samples from below the Pacific Ocean with the support of the Integrated Ocean Drilling Program. They collected sediments that were up to 16 million years old from 400 metres under the floor. The group then ran tests on the samples to detect the presence of ribosomal RNA from bacteria. As a genetic molecule that breaks down quickly after being produced, this RNA is a sign of living cells, and the tests found substantial quantities of it. verall, about 10-30% of the cells in ocean sediment are alive. According to their calculations, populations of bacteria living beneath the ocean floor multiply at a rate similar to those in surface environments. So how could these bacteria get so deep beneath the ocean floor? The only reasonable way is for them to be buried there. This means that colonies of bacteria have been surviving down there for millions of years. These microorganisms seem to produce significant amounts of methane through a metabolic process that does not rely on oxygen. Exactly how much of the global-warming gas is produced by the sub-seafloor population is not yet known. The discovery of thriving bacteria at great depths has other, more far-reaching implications. The cold temperatures and high pressures under which these marine bacteria survive lend support to the idea that life could exist in extreme conditions on other planets. It's well known that bacteria living in deep oceans have special adaptations that help them survive
Web resources : Federal Institute for Geosciences and Natural Resources
- hypogravity (< 1g) : halophiles are the first example of a vegetative cell surviving exposure to the space environment for two weeks and probably much longer.
- normogravity (1g)
- hypergravity (< 1g)
- halophiles. Some Bacteria (Staphylococci, Halobacteriacee, Ectothiorhodospira halochloris, Cyanobacteria (Aphanothece halophytica, Phormidium sp. and Schizothrix arenaria)), green Algae (Dunaliella salina and Asteromonas gracilis), diatoms (Amphora coffeaeformis, some species of Navicula and Nitzschia) and Protozoa (Blepharisma halophila and species of Bodo, Phyllomitus and Tetramites) can withstand periods in 25÷33 % Na+Cl-. With the exception of Halobacteriacee, which use K+ as their osmoticum, glycine betaine is the most effective osmoticum in most Prokarya, while Dunaliella salina uses glycerol. Although highly controversial, Bacteria might survive for millions of years in the fluid inclusions of salt deposits including evaporites (halite Na+Cl- + gypsum CaSO4.2H2O + anhydrite CaSO4).
- Haloquadratum walsbyi (Walsby's square archaeon) was discovered in a hypersaline pond near the Red Sea in 1980. The bacteria are around 0.15 mm across and have a remarkable shape, forming wafer-thin, regular tiles : it has resisted being cultured until in 2004 it was discovered it grows in very low concentrations of nutrients in hypersaline (>18% salt) solutionsref. The square haloarchaea of Walsby (SHOW group) dominate hypersaline microbial communities but have not been cultured since their discovery 25 years ago. Researchers showed that natural water dilution cultures can be used to isolate members of this group and, once in pure culture, they can be grown in standard halobacterial media. Cells display a square morphology and contain gas vesicles and poly-b-hydroxybutyrate (PHB) granules. The 16S rRNA gene sequence was >99% identical to other SHOW group sequences. They prefer high salinities (23–30%), and can grow with a doubling time of 1–2 days in rich media. The ability to culture SHOW group organisms makes it possible to study, in a comprehensive way, the microbial ecology of salt lakesref. In conditions with more nutrients, other species grow faster and swamp the slow-growing squares. And the saltier the sample used to start the culture the better, because this enhances the chance that the square bacteria will have survived in greater numbers than the other microbes have. The feat also takes plenty of patience. It took Bolhuis's team 2.5 years to get a pure culture. This is because the microbes grow extremely slowly, taking 1 to 2 days to double in number. By contrast, the lab workhorse Escherichia coli replicates in just 20 minutes. The microbe is also extremely tolerant of MgCl2 (> 2 M) in the presence of 3.3 M NaCl : this makes it a model organism for studying what life might be like in extraterrestrial corners of the solar system, such as the magnesium-rich brines on Jupiter's moons Europa and Ganymede. Fresh cultures contained extraordinary large cells (>40 x 40 µm) without any visible division structures, ranking them among the largest prokaryotes known to date. The genome was estimated to contain approximately 3 million bp. A community of microorganisms has been discovered in one of the saltiest environments on Earth, ultra-saturated salt basins deep in the Mediterranean Sea. The salt solution there is so concentrated, microbiologists are mystified as to how the organisms are able to survive. About 6 million years ago, the Mediterranean had dried up, having been separated from the Atlantic Ocean. Over time, sediment covered the salty deposits in the desolate basin. Eventually the area was reconnected with the Atlantic and filled with water again. Now, places where these underwater salty deposits are exposed are exceptionally briny, containing up to 476 grams of magnesium chloride (MgCl2) per litre. It was assumed that life could not exist in such conditions. The dense, viscous brine, which is twice as salty as soy sauce, would inexorably suck water molecules out of any cell. 4 such locations in the Mediterranean sea: l'Atalante, Bannock, Discovery and Urania salt basins, which are up to 500 m beneath the surface. The work was carried out as part of the BioDeep project, a collaboration of research groups across Europe. The researchers sent a robotic submarine down to retrieve water samples from the basins. When they analysed the samples, they were excited to find DNA, proving that microorganisms do exist there. So long as water is present in an environment, there appear to be few real limits to microbial life. Calcium chloride brines, such as Don Juan Pond in Antarctica, are now the only hypersaline environment in which life has yet to be found. The team sequenced the DNA fragments they retrieved, and discovered around 50 previously unknown species of bacteria, as well as 20 new species of archaea. They can exist in some of the planet's most hostile environments, such as thermal vents, and are thought to resemble the most ancient forms of life. The species the team found are very different from known archaeal species, and may belong to a separate evolutionary branch within the group. The researchers now hope to isolate live samples of the microorganisms from the basins and grow them in the lab, to get a better idea of how they function. Further investigation of the proteins and enzymes used by the microbes could prove useful for industry and biotech companies, who are always seeking ways to carry out reactions under extreme conditions. The existence of these hardy microbes lends support to the idea that life might exist in similar briny spots known to exist on other planets.
- acidophiles : Cyanidium caldarium has been described from nature at pH 0.5, Dunaliella acidophila at pH 1, Acontium cylatium, Cephalosporium sp. and Trichosporon cerebriae near pH 0, Picrophilus oshimae and Picrophilus torridus (thermophlici archaeans from Japanese solfataras) at pH 0.7, Ferroplasma acidarmanus at pH 0. The first 2 organism have cytoplasms at pH 7 thanks to membrane associated antiporters, positive surface charges and high internal buffer capacity : so only extracellular exposed proteins are acid-tolerant.
- alkaliphiles : representatives of all domains are able to tolerate pH 10.5 : Natronobacterium, Bacillus firmus OF4, Spirulina spp. in Lake Nakuru and Lake Simbi. Batrachoididae gen.sp. (toadfish) is very resistant to ammonia.
: Deinococcus
radiodurans can resist up to 20 kGy of g
radiations
when in logarithmic phase growth, high [Mn2+], [nutrients] and
Aw by using a unique DNA repair system. It was discovered around
50 years ago in a batch of irradiated meat. The most resistant bacteria
tend to store up high levels of manganese and relatively low levels of
iron; by contrast, the bacteria that shrivel up at a hint of radiation
have little manganese and more ironref.
Manganese helps to clear up damaging molecules, such as free radicals,
that are released by the bugs' metabolism. This leaves the bacteria in
a healthier state and better able to patch up DNA damaged by radiation.
A dose of antioxidants that mimic some of the effects of manganese, such
as vitamin E, might safeguard the cells of those who are exposed to radiation
by a nuclear accident, for example. But radiation-resistant bacteria might
have high manganese for another reason unconnected to their hardiness.
Some proposed that peculiar circular rings of DNA in the bacteria help
them patch up their damaged DNAref,
but others grew bacteria in which these rings were missing and showed that
they were just as hardy. The bacterium Deinococcus radiodurans is
the best known extremophile among the few organisms that can survive extremely
high exposures to desiccation and ionizing radiation, which shatter its
genome into hundreds of short DNA fragments. Remarkably, these fragments
are readily reassembled into a functional 3.28-megabase genome. The relevant
2-stage DNA repair process, which involves a previously unknown molecular
mechanism for fragment reassembly called 'extended synthesis-dependent
strand annealing' (ESDSA), followed and completed by crossovers. At
least 2 genome copies and random DNA breakage are requirements for effective
ESDSA. In ESDSA, chromosomal fragments with overlapping homologies are
used both as primers and as templates for massive synthesis of complementary
single strands, as occurs in a single-round multiplex polymerase chain
reaction. This synthesis depends on DNA polymerase I and incorporates more
nucleotides than does normal replication in intact cells. Newly synthesized
complementary single-stranded extensions become 'sticky ends' that anneal
with high precision, joining together contiguous DNA fragments into long,
linear, double-stranded intermediates. These intermediates require RecA-dependent
crossovers to mature into circular chromosomes that comprise double-stranded
patchworks of numerous DNA blocks synthesized before radiation, connected
by DNA blocks synthesized after radiationref- metalotolerant : Ferroplasma acidarmanus resists high levels of Cu, As, Cd and Zn. Ralstonia sp.CH34 resists Zn, Co, Cd, Hg, Pb removing them through efflux pump.
-
metalosensitive : e.g. Shigella
spp.
