The Energetics of Chemolithotrophy
Chemolithotrophs use electron donors oxidized in the cell, and channel electrons into respiratory chains, producing ATP.
Outline the characteristics associated with chemolithotrophs
- Chemotrophs are organisms that obtain energy by the oxidation of electron donors in their environments. These molecules can be organic (chemoorganotrophs) or inorganic ( chemolithotrophs ).
- In chemolithotrophs, the compounds – the electron donors – are oxidized in the cell, and the electrons are channeled into respiratory chains, ultimately producing ATP.
- The electron acceptor can be oxygen (in aerobic bacteria ), but a variety of other electron acceptors, organic and inorganic, are also used by various species.
- chemolithotroph: chemoautotroph
- symbiont: An organism that lives in a symbiotic relationship; a symbiote.
- chemotroph: an organism that obtains energy by the oxidation of electron-donating molecules in the environment
- lithotroph: An organism that obtains its energy from inorganic compounds (such as ammonia) via electron transfer.
A lithotroph is an organism that uses an inorganic substrate (usually of mineral origin) to obtain reducing equivalents for use in biosynthesis (e.g., carbon dioxide fixation) or energy conservation via aerobic or anaerobic respiration. Known chemolithotrophs are exclusively microbes; no known macrofauna possesses the ability to utilize inorganic compounds as energy sources. Macrofauna and lithotrophs can form symbiotic relationships, in which case the lithotrophs are called “prokaryotic symbionts”. An example of this is chemolithotrophic bacteria in deep sea worms or plastids, which are organelles within plant cells that may have evolved from photolithotrophic cyanobacteria-like organisms.
Chemotrophs are organisms that obtain energy through the oxidation of electron donors in their environments. These molecules can be organic (chemoorganotrophs) or inorganic (chemolithotrophs). The chemotroph designation is in contrast to phototrophs, which utilize solar energy. Chemotrophs can be either autotrophic or heterotrophic. Chemoautotrophs generally fall into several groups: methanogens, halophiles, sulfur oxidizers and reducers, nitrifiers, anammox bacteria, and thermoacidophiles. Chemolithotrophic growth could be dramatically fast, such as Thiomicrospira crunogena with a doubling time around one hour.
In chemolithotrophs, the compounds – the electron donors – are oxidized in the cell, and the electrons are channeled into respiratory chains, ultimately producing ATP. The electron acceptor can be oxygen (in aerobic bacteria), but a variety of other electron acceptors, organic and inorganic, are also used by various species. Unlike water, the hydrogen compounds used in chemosynthesis are high in energy. Other lithotrophs are able to directly utilize inorganic substances, e.g., iron, hydrogen sulfide, elemental sulfur, or thiosulfate, for some or all of their energy needs.
While there are several mechanisms of anaerobic hydrogen oxidation, organisms can also use hydrogen as an energy source aerobically.
Discuss the process of hydrogen oxidation in organisms that use hydrogen aerobically
- In some organisms, hydrogen is oxidized by a membrane-bound hydrogenase causing proton pumping via electron transfer to various quinones and cytochromes.
- Hydrogen-oxidizing organisms, such as Cupriavidus necator (formerly Ralstonia eutropha), often inhabit oxic-anoxic interfaces in nature to take advantage of the hydrogen produced by anaerobic fermentative organisms while still maintaining a supply of oxygen.
- Helicobacter pylori is a Gram-negative, microaerophilic bacterium found in the stomach. It has been postulated that it may play an important role in the natural stomach ecology.
- Knallgas-bacteria: Bacteria which oxidize hydrogen.
- calvin cycle: A series of biochemical reactions that take place in the stroma of chloroplasts in photosynthetic organisms.
Chemolithotrophy is a type of metabolism where energy is obtained from the oxidation of inorganic compounds. Most chemolithotrophic organisms are also autotrophic. There are two major objectives to chemolithotrophy: the generation of energy (ATP) and the generation of reducing power (NADH).
Hydrogen oxidizing bacteria, or sometimes Knallgas-bacteria, are bacteria that oxidize hydrogen. These bacteria include Hydrogenobacter thermophilus, Hydrogenovibrio marinus, and Helicobacter pylori. There are both Gram positive and Gram negative knallgas bacteria.
Most grow best under microaerophilic conditions. They do this because the hydrogenase enzyme used in hydrogen oxidation is inhibited by the presence of oxygen, but oxygen is still needed as a terminal electron acceptor.
Many organisms are capable of using hydrogen (H2) as a source of energy. While there are several mechanisms of anaerobic hydrogen oxidation (e.g. sulfate reducing- and acetogenic bacteria), hydrogen can also be used as an energy source aerobically. In these organisms, hydrogen is oxidized by a membrane-bound hydrogenase causing proton pumping via electron transfer to various quinones and cytochromes. In many organisms, a second cytoplasmic hydrogenase is used to generate reducing power in the form of NADH, which is subsequently used to fix carbon dioxide via the Calvin cycle. Hydrogen-oxidizing organisms, such as Cupriavidus necator (formerly Ralstonia eutropha), often inhabit oxic-anoxic interfaces in nature to take advantage of the hydrogen produced by anaerobic fermentative organisms while still maintaining a supply of oxygen.
Helicobacter pylori (H. pylori ), previously named Campylobacter pyloridis, is a Gram-negative, microaerophilic bacterium found in the stomach. It was identified in 1982 by Barry Marshall and Robin Warren. They found that it was present in patients with chronic gastritis and gastric ulcers, conditions that were not previously believed to have a microbial cause. It is also linked to the development of duodenal ulcers and stomach cancer. However, over 80 percent of individuals infected with the bacterium are asymptomatic. It has been postulated that it may play an important role in the natural stomach ecology. More than 50% of the world’s population harbor H. pylori in their upper gastrointestinal tract. Infection is more prevalent in developing countries and incidence is decreasing in Western countries. H. pylori’s helix shape (from which the generic name is derived) is thought to have evolved to penetrate the mucoid lining of the stomach.
Oxidation of Reduced Sulfur Compounds
Sulfur oxidation involves the oxidation of reduced sulfur compounds, inorganic sulfur, and thiosulfate to form sulfuric acid.
Describe the process of sulfur oxidation
- The oxidation of sulfide occurs in stages, with inorganic sulfur being stored either inside or outside of the cell until needed.
- This two step process occurs because sulfide is a better electron donor than inorganic sulfur or thiosulfate; this allows a greater number of protons to be translocated across the membrane.
- Sulfur-oxidizing organisms generate reducing power for carbon dioxide fixation via the Calvin cycle using reverse electron flow—an energy-requiring process that pushes the electrons against their thermodynamic gradient to produce NADH.
- calvin cycle: A series of biochemical reactions that take place in the stroma of chloroplasts in photosynthetic organisms.
- thiosulfate: Any salt or ester of thiosulfuric acid.
- chemolithoautotrophic: The characteristic of a microorganism that obtains energy from the oxidation of inorganic compounds and carbon from the fixation of carbon dioxide.
Sulfur is an essential element for all life, and it is widely used in biochemical processes. In metabolic reactions, sulfur compounds serve as both fuels and respiratory (oxygen-alternative) materials for simple organisms. Sulfur is an important part of many enzymes and antioxidant molecules such as glutathione and thioredoxin.
Sulfur oxidation involves the oxidation of reduced sulfur compounds such as sulfide (H2S), inorganic sulfur (S0), and thiosulfate (S2O2−3) to form sulfuric acid (H2SO4). An example of a sulfur-oxidizing bacterium is Paracoccus.
Generally, the oxidation of sulfide occurs in stages, with inorganic sulfur being stored either inside or outside of the cell until needed. The two step process occurs because sulfide is a better electron donor than inorganic sulfur or thiosulfate; this allows a greater number of protons to be translocated across the membrane. Sulfur-oxidizing organisms generate reducing power for carbon dioxide fixation via the Calvin cycle using reverse electron flow—an energy-requiring process that pushes the electrons against their thermodynamic gradient to produce NADH. Biochemically, reduced sulfur compounds are converted to sulfite (SO2−3) and, subsequently, sulfate (SO2−4) by the enzyme sulfite oxidase. Some organisms, however, accomplish the same oxidation using a reversal of the APS reductase system used by sulfate-reducing bacteria (see above). In all cases the energy liberated is transferred to the electron transport chain for ATP and NADH production. In addition to aerobic sulfur oxidation, some organisms (e.g. Thiobacillus denitrificans) use nitrate (NO−3) as a terminal electron acceptor and therefore grow anaerobically.
A classic example of a sulfur-oxidizing bacterium is Beggiatoa, a microbe originally described by Sergei Winogradsky, one of the founders of environmental microbiology. Beggiatoa can be found in marine or freshwater environments. They can usually be found in habitats that have high levels of hydrogen sulfide. These environments include cold seeps, sulfur springs, sewage contaminated water, mud layers of lakes, and near deep hydrothermal vents. Beggiatoa can also be found in the rhizosphere of swamp plants. During his research in Anton de Bary’s laboratory of botany in 1887, Russian botanist Winogradsky found that Beggiatoa oxidized hydrogen sulfide (H2S) as an energy source, forming intracellular sulfur droplets. Winogradsky referred to this form of metabolism as inorgoxidation (oxidation of inorganic compounds). The finding represented the first discovery of lithotrophy.
Beggiatoa can grow chemoorgano-heterotrophically by oxidizing organic compounds to carbon dioxide in the presence of oxygen, though high concentrations of oxygen can be a limiting factor. Organic compounds are also the carbon source for biosynthesis. Some species may oxidize hydrogen sulfide to elemental sulfur as a supplemental source of energy (facultatively litho-heterotroph). This sulfur is stored intracellularly. Some species have the ability of chemolithoautotrophic growth, using sulfide oxidation for energy and carbon dioxide as a source of carbon for biosynthesis. In this metabolic process, internal stored nitrate is the electron acceptor and reduced to ammonia.
Sulfide oxidation: 2H2S + O2 → 2S + 2H2O
Marine autotrophic Beggiatoa species are able to oxidize intracellular sulfur to sulfate. The reduction of elemental sulfur frequently occurs when oxygen is lacking. Sulfur is reduced to sulfide at the cost of stored carbon or by added hydrogen gas. This may be a survival strategy to bridge periods without oxygen
Ferric iron is an anaerobic terminal electron acceptor, with the final enzyme a ferric iron reductase.
Outline the purpose of iron oxidation and the three types of ferrous iron-oxidizing microbes (acidophiles, microaerophiles and anaerobic photosynthetic bacteria)
- Ferrous iron is a soluble form of iron that is stable at extremely low pHs or under anaerobic conditions. Under aerobic, moderate pH conditions ferrous iron is oxidized spontaneously to the ferric (Fe3+) form and is hydrolyzed abiotically to insoluble ferric hydroxide (Fe(OH)3).
- Three distinct types of ferrous iron-oxidizing microbes: acidophiles, microaerophiles that oxidize ferrous iron at cirum-neutral pH, anaerobic photosynthetic bacteria which use ferrous iron to produce NADH for autotrophic carbon dioxide fixation.
- Although ferric iron is the most prevalent inorganic electron acceptor, a number of organisms can use other inorganic ions in anaerobic respiration.
- autotroph: Any organism that can synthesize its food from inorganic substances, using heat or light as a source of energy.
- heterotroph: An organism that requires an external supply of energy in the form of food as it cannot synthesize its own.
Ferric iron (Fe3+) is a widespread anaerobic terminal electron acceptor both for autotrophic and heterotrophic organisms. Electron flow in these organisms is similar to those in electron transport, ending in oxygen or nitrate, except that in ferric iron-reducing organisms the final enzyme in this system is a ferric iron reductase. Model organisms include Shewanella putrefaciens and Geobacter metallireducens. Since some ferric iron-reducing bacteria (e.g. G. metallireducens) can use toxic hydrocarbons such as toluene as a carbon source, there is significant interest in using these organisms as bioremediation agents in ferric iron-rich contaminated aquifers.
Ferrous iron is a soluble form of iron that is stable at extremely low pHs or under anaerobic conditions. Under aerobic, moderate pH conditions ferrous iron is oxidized spontaneously to the ferric (Fe3+) form and is hydrolyzed abiotically to insoluble ferric hydroxide (Fe(OH)3). There are three distinct types of ferrous iron-oxidizing microbes. The first are acidophiles, such as the bacteria Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans, as well as the archaeon Ferroplasma. These microbes oxidize iron in environments that have a very low pH and are important in acid mine drainage. The second type of microbes oxidizes ferrous iron at cirum-neutral pH. These micro-organisms (for example Gallionella ferruginea or Leptothrix ochracea) live at the oxic-anoxic interfaces and are microaerophiles. The third type of iron-oxidizing microbes is anaerobic photosynthetic bacteria such as Rhodopseudomonas, which use ferrous iron to produce NADH for autotrophic carbon dioxide fixation. Biochemically, aerobic iron oxidation is a very energetically poor process which therefore requires large amounts of iron to be oxidized by the enzyme rusticyanin to facilitate the formation of proton motive force. Like sulfur oxidation, reverse electron flow must be used to form the NADH used for carbon dioxide fixation via the Calvin cycle.
Although ferric iron is the most prevalent inorganic electron acceptor, a number of organisms (including the iron-reducing bacteria mentioned above) can use other inorganic ions in anaerobic respiration. While these processes may often be less significant ecologically, they are of considerable interest for bioremediation, especially when heavy metals or radionuclides are used as electron acceptors. Examples include:
- Manganic ion (Mn4+) reduction to manganous ion]] (Mn2+)
- Selenate (SeO2−4) reduction to selenite (SeO2−3) and selenite reduction to inorganic selenium (Se0)
- Arsenate (AsO3−4) reduction to arsenite (AsO3−3)
- Uranyl ion ion (UO2+2) reduction to uranium dioxide (UO2)
Nitrification is the process by which ammonia (NH3) or ammonium (NH4+) is converted to nitrite (NO2–) and then nitrate (NO3−) by bacteria.
Describe the process of nitrification and its importance
- Nitrification is actually the net result of two distinct processes: the oxidation of ammonia (NH3) or ammonium (NH4+) to nitrite (NO2−) by ammonia-oxidizing bacteria (e.g. Nitrosomonas) and the oxidation of nitrite (NO2–) to nitrate (NO3–) by the nitrite-oxidizing bacteria (e.g. Nitrobacter).
- Nitrification is extremely energetically poor leading to very slow growth rates for both types of organisms.
- Oxygen is required in ammonium and nitrite oxidation; ammonia-oxidizing and nitrite-oxidizing bacteria are aerobes.
- chemolithotrophy: A type of metabolism where energy is obtained from the oxidation of inorganic compounds.
- nitrification: The biological oxidation of ammonia or ammonium with oxygen into nitrite followed by the oxidation of these nitrites into nitrates.
Process of Nitrification
Nitrification is the process by which ammonia (NH3) or ammonium (NH4+) is converted to nitrate (NO3−). Nitrification is the net result of two distinct processes: oxidation of ammonium to nitrite (NO2−) by nitrosifying or ammonia-oxidizing bacteria and oxidation of nitrite (NO2−) to nitrate (NO3−) by the nitrite-oxidizing bacteria. Nitrification is an important step in the nitrogen cycle in soil. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea.
Chemistry of Nitrogen Compound Oxidation
Nitrification is a process of nitrogen compound oxidation (effectively, loss of electrons from the nitrogen atom to the oxygen atoms):
- 2 NH4+ + 3 O2 → 2 NO2– + 2 H2O + 4 H+ (Nitrosomonas)
- 2 NO2– + O2 → 2 NO3– (Nitrobacter, Nitrospina)
- NH3 + O2 → NO2− + 3H+ + 2e−
- NO2− + H2O → NO3− + 2H+ + 2e−
Both of these processes are extremely energetically poor, which leads to very slow growth rates for both types of organisms.
The transformation of ammonia to nitrite is usually the rate limiting step of nitrification. Biochemically, ammonium oxidation occurs by the stepwise oxidation of ammonium to hydroxylamine (NH2OH) by the enzyme ammonium monooxygenase in the cytoplasm, followed by the oxidation of hydroxylamine to nitrite by the enzyme hydroxylamine oxidoreductase in the periplasm. Electron and proton cycling are very complex, but as a net result only one proton is translocated across the membrane per molecule of ammonium oxidized.
Nitrite reduction is much simpler, with nitrite being oxidized by the enzyme nitrite oxidoreductase coupled to proton translocation by a very short electron transport chain, again leading to very low growth rates for these organisms. Oxygen is required in ammonium and nitrite oxidation, meaning that both nitrosifying and nitrite-oxidizing bacteria are aerobes. As in sulfur and iron oxidation, NADH for carbon dioxide fixation using the Calvin cycle is generated by reverse electron flow, thereby placing a further metabolic burden on an already energy-poor process.
Human Applications of Nitrification
Nitrification is important in agricultural systems, where fertilizer is often applied as ammonia. Nitrification also plays an important role in the removal of nitrogen from municipal wastewater. The conventional removal is nitrification, followed by denitrification.
Anammox, an abbreviation for ANaerobic AMMonium OXidation, is a globally significant microbial process of the nitrogen cycle.
Describe the overall process of ANaerobic AMMonium OXidation (Anammox) and its purpose
- The bacteria mediating this process were identified in 1999, and at the time were a great surprise for the scientific community.
- This form of metabolism occurs in members of the Planctomycetes (e.g. Candidatus Brocadia anammoxidans) and involves the coupling of ammonia oxidation to nitrite reduction.
- To deal with the high toxicity of hydrazine, anammox bacteria contain a hydrazine-containing intracellular organelle called the anammoxasome, surrounded by highly compact ladderane lipid membrane. These lipids are unique in nature, as is the use of hydrazine as a metabolic intermediate.
- Anammox: An abbreviation for ANaerobic AMMonium OXidation, a globally significant microbial process of the nitrogen cycle.
- anaerobes: Organisms that do not require oxygen for growth.
- ladderane: Any of a class of polycyclic hydrocarbons, consisting of repeating cyclobutane moieties, that resemble ladders
Anammox, an abbreviation for ANaerobic AMMonium OXidation, is a globally significant microbial process of the nitrogen cycle. The bacteria mediating this process were identified in 1999, and at the time were a great surprise to the scientific community. Anammox takes place in many natural environments, contributing up to 50% of the dinitrogen gas produced in the oceans. In this biological process, nitrite and ammonium are converted directly into dinitrogen gas. The overall catabolic reaction is:
NH4+ + NO2− → N2 + 2H2O.
This form of metabolism involves the coupling of ammonia oxidation to nitrite reduction. Since oxygen is not required for the process, these organisms are strict anaerobes. Amazingly, hydrazine (N2H4 — rocket fuel) is produced as an intermediate during anammox metabolism. To deal with the high toxicity of hydrazine, anammox bacteria have a hydrazine-containing intracellular organelle called the anammoxasome (a compartment inside the cytoplasm which is the locus of anammox catabolism), which is surrounded by an unusual and highly compact ladderane lipid membrane. Further, the membranes of these bacteria mainly consist of ladderane lipids so far unique in biology. Of special interest is the conversion to hydrazine (normally used as a high-energy rocket fuel, and poisonous to most living organisms) as an intermediate. A final striking feature of the organism is the extremely slow growth rate. The doubling time is nearly two weeks. The anammox process was originally found to occur only from 20°C to 43°C but more recently, anammox has been observed at temperatures from 36°C to 52°C in hot springs and 60°C to 85°C at hydrothermal vents located along the Mid-Atlantic Ridge.
Anammox organisms are autotrophs although the mechanism for carbon dioxide fixation is still unclear. Because of this property, these organisms could be used industrially to remove nitrogen in wastewater treatment processes. The bacteria that perform the anammox process belong to the bacterial phylum Planctomycetes (e.g. Candidatus Brocadia anammoxidans), of which Planctomyces and Pirellula are the best known genera. Currently five genera of anammox bacteria have been (provisionally) defined: Brocadia, Kuenenia, Anammoxoglobus, Jettenia (all fresh water species), and Scalindua (marine species).
Rhodobacter sphaeroides is able to produce hydrogen from a wide range of organic compounds (chiefly organic acids) and light.
List a function of Rhodococcus in the scientific community
- In the absence of water-splitting, photosynthesis is anoxygenic. Therefore, hydrogen production is sustained without inhibition from generated oxygen.
- Strains of Rhodococcus are applicably important owing to their ability to catabolize a wide range of compounds and produce bioactive steroids, acrylamide, and acrylic acid, and their involvement in fossil fuel biodesulfurization.
- The use of Rhodococcus is borne out of its ability to metabolize harmful environmental pollutants, such as toluene, naphthalene, herbicides, and PCBs.
- catabolism: Destructive metabolism, usually includes the release of energy and breakdown of materials.
- Rhodococcus: a genus of aerobic, nonsporulating, nonmotile Gram-positive bacteria closely related to Mycobacteria and Corynebacteria.
- benzoate: Any salt or ester of benzoic acid.
Benzoate catabolism is a series of chemical reactions resulting in the breakdown of benzoate. The purple non-sulphur (PNS) bacteria Rhodobacter sphaeroides is able to produce hydrogen from a wide range of organic compounds (chiefly organic acids) and light. The photo-system required for hydrogen production in Rhodobacter (PS-I) differ from its oxygenic photosystem (PS-II) due to the requirement of organic acids and the inability to oxidize water. In the absence of water-splitting, photosynthesis is anoxygenic. Therefore, hydrogen production is sustained without inhibition from generated oxygen. In PNS bacteria, hydrogen production is due to catalysis by nitrogenase. Hydrogenases are also present but the production of hydrogen by [FeFe]-hydrogenase is less than ten times the hydrogen uptake by [NiFe]-hydrogenase. Only under nitrogen-deficient conditions is nitrogenase activity sufficient to overcome uptake hydrogenase activity, resulting in net generation of hydrogen.
Rhodococcus is a genus of aerobic, nonsporulating, nonmotile Gram-positive bacteria closely related to Mycobacteria and Corynebacteria. While a few species are pathogenic, most are benign and have been found to thrive in a broad range of environments, including soil, water, and eukaryotic cells. Fully sequenced in October 2006, the genome is known to be 9.7 megabasepairs long and 67% G/C. Strains of Rhodococcus are applicably important owing to their ability to catabolize a wide range of compounds and produce bioactive steroids, acrylamide, and acrylic acid, and their involvement in fossil fuel biodesulfurization. This genetic and catabolic diversity is not only due to the large bacterial chromosome, but also to the presence of three large linear plasmids. Rhodococcus is also an experimentally advantageous system owing to a relatively fast growth rate and simple developmental cycle. However, as it stands now, Rhodococcus is not well characterized. Another important application of Rhodococcus comes from bioconversion, using biological systems to convert cheap starting material into more valuable compounds. This use of Rhodococcus is borne out of its ability to metabolize harmful environmental pollutants, such as toluene, naphthalene, herbicides, and PCBs. Rhodococci typically metabolize aromatic substrates by first oxygenating the aromatic ring to form a diol (two alcohol groups). Then, the ring is cleaved with intra/extradiol mechanisms, opening the ring and exposing the substrate to further metabolism. Since the chemistry here is very stereospecific, the diols are created with predictable chirality. While controlling the chirality of chemical reaction presents a significant challenge for synthetic chemists, biological processes can be used instead to faithfully produce chiral molecules in cases where direct chemical synthesis is infeasible or inefficient. An example of this is the use of Rhodococcus to produce indene, a precursor to the AIDS drug CrixivanTM, a protease inhibitor, and containing two of the five chiral centers needed in the complex.
Polycyclic Aromatic Hydrocarbons
Polycyclic aromatic hydrocarbons are potent atmospheric pollutants that consist of fused aromatic rings and do not contain heteroatoms.
Recognize various sources of polycyclic aromatic hydrocarbons and means of removal (bio-, phy
- Polycyclic aromatic hydrocarbons (PAHs) occur in oil, coal, and tar deposits, and they are produced as byproducts of fuel burning (whether fossil fuel or biomass ).
- Bioremediation is the use of microorganism metabolism to remove pollutants. These technologies can be generally classified as in situ or ex situ.
- Mycoremediation is a form of bioremediation that uses fungi to degrade or sequester contaminants in the environment. Stimulating microbial and enzyme activity, mycelium reduces toxins in situ.
- Polycyclic aromatic hydrocarbons: also known as poly-aromatic hydrocarbons or polynuclear aromatic hydrocarbons, are potent atmospheric pollutants that consist of fused aromatic rings and do not contain heteroatoms or carry substituents.
- carcinogenic: Causing or tending to cause cancer.
- mutagenic: Capable of causing mutation.
Polycyclic aromatic hydrocarbons (PAHs), also known as poly-aromatic hydrocarbons or polynuclear aromatic hydrocarbons, are seen in. PAHs are potent atmospheric pollutants that consist of fused aromatic rings and do not contain heteroatoms or carry substituents. Naphthalene is the simplest example of a PAH. PAHs occur in oil, coal, and tar deposits, and are produced as byproducts of fuel burning (whether fossil fuel or biomass). As a pollutant, they are of concern because some compounds have been identified as carcinogenic, mutagenic, and teratogenic. PAHs are also found in cooked foods—studies have found PAHs in meat cooked at high temperatures such as grilling or barbecuing, and in smoked fish. They are also found in the interstellar medium, comets, and meteorites. PAHs are a candidate for the molecule acted as a basis for the earliest forms of life. In graphene the PAH motif is extended to large 2D sheets.
Natural crude oil and coal deposits contain significant amounts of PAHs from chemical conversion of natural product molecules, such as steroids, to aromatic hydrocarbons. They are also found in processed fossil fuels, tar, and various edible oils.
Phospholipid -derived fatty acids (PLFA) are widely used in microbial ecology as chemotaxonomic markers of bacteria and other organisms. Phospholipids are the primary lipids composing cellular membranes. They can be esterified to many types of fatty acids. Once the phospholipids of an unknown sample are esterfied, the composition of the resulting PLFA can be compared to the PLFA of known organisms to determine the identity of the sample organism. PLFA analysis may be combined with stable isotope probing to determine which microbes are metabolically active in a sample.
The basic premise for PLFA analysis is that as individual organisms (especially bacteria and fungi) die, phospholipids are rapidly degraded and the remaining phospholipid content of the sample is assumed to be from living organisms. As the phospholipids of different groups of bacteria and fungi contain a variety of somewhat unique fatty acids, they can serve as useful biomarkers for such groups. PLFA profiles and composition can be determined by purifying the phospholipids and then cleaving the fatty acids for further analysis.
Bioremediation is the use of micro-organism metabolism to remove pollutants. Technologies can be generally classified as in situ or ex situ. In situ bioremediation involves treating the contaminated material at the site, while ex situ involves the removal of the contaminated material to be treated elsewhere. Some examples of bioremediation related technologies are phytoremediation, bioventing, bioleaching, landfarming, bioreactor, composting, bioaugmentation, rhizofiltration, and biostimulation.
Bioremediation can occur on its own (natural attenuation or intrinsic bioremediation) or can be spurred on via the addition of fertilizers to increase the bioavailability within the medium (biostimulation). Recent advancements have found success by adding matched microbe strains to the medium to enhance the resident microbe population ‘s ability to break down contaminants. Microorganisms used to perform the function of bioremediation are known as bioremediators. Not all contaminants, however, are easily treated by bioremediation using microorganisms. For example, heavy metals such as cadmium and lead are not readily absorbed or captured by microorganisms. The assimilation of metals such as mercury into the food chain may worsen matters.
Phytoremediation is useful in these circumstances because natural plants or transgenic plants are able to bioaccumulate these toxins in their above-ground parts, which are then harvested for removal. The heavy metals in the harvested biomass may be further concentrated by incineration or recycled for industrial use. The elimination of a wide range of pollutants and wastes from the environment requires increasing our understanding of the relative importance of different pathways and regulatory networks to carbon flux in particular environments and for particular compounds, and they will certainly accelerate the development of bioremediation technologies and biotransformation processes.
Mycoremediation, is a form of bioremediation, the process of using fungi to degrade or sequester contaminants in the environment. Stimulating microbial and enzyme activity, mycelium reduces toxins in situ. Some fungi are hyperaccumulators, capable of absorbing and concentrating heavy metals in the mushroom fruit bodies. One of the primary roles of fungi in the ecosystem is decomposition, which is performed by the mycelium. The mycelium secretes extracellular enzymes and acids that break down lignin and cellulose, the two main building blocks of plant fiber. These organic compounds are composed of long chains of carbon and hydrogen, structurally similar to many organic pollutants. The key to mycoremediation is determining the right fungal species to target a specific pollutant.
Gallaecimonas is a recently described genus of bacteria. It is a Gram-negative, rod-shaped, halotolerant bacterium in the class Gammaproteobacteria. It can degrade high molecular mass polycyclic aromatic hydrocarbons of 4 and 5 rings. The 16S rRNA gene sequences of the type strain CEE_131(T) proved to be distantly related to those of Rheinheimera and Serratia.