compiled by
Eric A. Seagren, University of Maryland
David A. Stahl, Northwestern University
A:
Abiotic - Occurring without the involvement of microorganisms.
Accessory DNA elements - Plasmids, insertion elements, transposons, and some viruses are genetic elements that encode genes not essential to cellular reproduction and that are generally relatively freely passed between different organisms, including different species and genera.
Acclimation - See adaptation.
Acidophile - A microorganism that grows best at acidic pH values.
Adaptation - The process of adjustment by microbes to a specific set of environmental conditions. Period during which a microbial population is "gearing up" for metabolism and degradation of a specific mix of pollutants or a specific organic compound. This is usually expressed as a lag phase when the organisms are growing at a slow rate and utilizing other substrates in preference to the target contaminant(s). When a critical biomass is reached in population numbers, the log growth phase begins in which the target contaminants are degraded. During adaptation, there may be temporary conditions of limited nutrients or environmental inhibitions that must be overcome by enzyme induction and other genetic accommodations. Synonym = acclimation
Adsorption - The physical adherence of solids or chemicals to another surface: a surface active phenomenon as opposed to an absorption in which a liquid is taken up by a solid medium, or a gas dissolves in liquid.
Advection - The process by which solutes are transported by the bulk motion of the flowing ground water.
Aerobe - A microorganism capable of growing in the presence of free oxygen, may be facultative or obligate.
Aerobic respiration - Process whereby microorganisms use oxygen as an electron acceptor to generate energy.
Air sparging - Injection of air into ground water to remove volatile chemicals and deliver oxygen, which promotes microbial growth.
Air stripping - Above-ground process used to remove volatile contaminants from water. It involves exposing the water surface to a large volume of air, usually by flowing water through a tower in one direction and air through the tower in the opposite direction.
Aliphatic hydrocarbon - A compound built from carbon and hydrogen joined in a linear chain. Petroleum products are composed primarily of aliphatic hydrocarbons.
Alkaliphile - An organism that grows best at high pH.
Anabolism - The biochemical processes involved in the synthesis of cell constituents from simpler molecules, usually requiring energy.
Anaerobe - A microorganism capable of growth in the absence of oxygen. Facultative anaerobes can, for example, use nitrate in the absence of oxygen. Strict anaerobes cannot abide the presence of any oxygen.
Anaerobic respiration - Process whereby microorganisms use a chemical other than oxygen as an electron acceptor. Common "substitutes" for oxygen are nitrate, sulfate, and iron.
Anoxic - Absence of oxygen. Usually used in reference to a microbial habitat.
API Separator - A process unit of American Petroleum Institute (API) approved standard design for separation of oil, floating debris, solids, and wastewater. These are massive impoundments that trap oily solids and skim floating oil from refinery generated wastewater. They are normally about 30 - 40 ft deep and can cover an acre in surface area.
Aquiclude - A relatively impermeable underground confining unit, such as a clay. These saturated geologic units are incapable of transmitting significant quantities of water under ordinary hydraulic gradients. Very few formations fit the classical definition of an aquiclude.
Aquifer - An underground saturated, permeable, geological formation that can transmit significant quantities of water under ordinary hydraulic gradients (see hydraulic gradient). The most common aquifers are unconsolidated sands and gravels, permeable sedimentary rocks such as sandstones and limestones, and heavily fractured volcanic and crystalline rocks. A confined aquifer is an aquifer that is confined between two confining beds, such as aquicludes or aquitards (see aquiclude and aquitard). An unconfined aquifer, or water-table aquifer, is an aquifer in which the water table forms the upper boundary (see water-table). Confined aquifers occur at depth, unconfined aquifers near the ground surface.
Aquitard - An underground confining unit characterized by low permeability that does not readily permit water to pass through it despite the fact that it stores large quantities of water. The most common aquitards are clays, shales, and dense crystalline rocks.
Archaea - An evolutionarily distinct group (domain) of prokaryotes consisting of the methanogens, most extreme halophiles and hyperthermophiles, and Thermoplasma.
Archaebacteria - An old term for the Archaea.
Aromatic hydrocarbon - A chemical formed from benzene rings, originally call "aromatic" because of benzene's distinctive aroma. Solvents, many types of pesticides, and polychlorinated biphenyls are composed of aromatic hydrocarbons.
Atmosphere - One Atm of pressure equals 14.7 lbs/sq in.
Autochthonous microorganisms - The indigenous or native microorganisms.
Autotroph - An organism having the capacity to "fix" inorganic carbon (CO2) [incorporate it into more reduced carbon compounds] and use CO2 as sole carbon source for growth.
B:
Bacteria - all prokaryotes that are not members of the domain Archaea.
Bacterium - The traditional name for a single-celled prokaryotic organism of microscopic size. Bacteria are ubiquitous in the environment, inhabiting water, soil, organic matter, and the bodies of plants and animals. Recent taxonomic restructuring of the prokaryotes has divided them into two distinct lines of evolutionary descent, the domains Archaea and Bacteria.
Barophile - An organism able to live optimally at high hydrostatic pressure.
Benzene - A chemical composed of six carbon atoms arranged in a hexagonal ring, with one hydrogen attached to each carbon.
Bioaccumulation - Biological uptake of an element or compound from solution in amounts up to its ambient concentration in the environment.
Bioaugmentation - The addition of microorganisms to a site. The added microorganisms may be nonnative or previously recovered from the site.
Biocurtain - A large quantity of organisms grown underground specifically to stop contaminant migration by creating localized clogging.
Biodegradation - Biologically mediated conversion of one compound to another; no extent is necessarily implied. Biodegradation need not have a benign outcome. For example, it could convert an innocuous chemical into a toxic one, or change a readily metabolizable compound into one difficult to destroy. Nevertheless, note that when scientists and engineers state that a chemical is biodegradable, they usually mean that it can be mineralized (see mineralization).
Biofilm - Microorganisms and extracellular products associated with a substratum.
Biogenic - Processes or products of biologic origin.
Biogeochemistry - Study of microbially mediated chemical transformations of geochemical interest, e.g. nitrogen or sulfur cycling.
Biomagnification - Biological uptake of an element or compound through biosorption and/or bioaccumulation in amounts over and above its ambient concentration in the environment, becoming a sink for that species by magnifying its concentration in living cells.
Biomass - Total mass of microorganisms present in a given amount of water or soil.
Bioremediation - Use of microorganisms to control and destroy contaminants.
Biosorption - External uptake of an element or compound by various selective ligands attached to the outer layer of the microbial cell membrane.
Biosynthesis - A general term for all the biochemical metabolic processes and pathways which synthesize cellular components necessary for the maintenance of life.
Bioventing - Circulation of air through the unsaturated subsurface to remove volatile contaminants and provide oxygen, which stimulates microorganisms to degrade remaining contaminants.
BOD - Biochemical oxygen demand; an estimate of the amount of organic carbon available for microbial transformation.
BTEX - Acronym for benzene, toluene, ethylbenzene, and xylenes, which are compounds present in gasoline and other petroleum products, coal tar, and various organic chemical product formulations.
C:
Carbon treatment - Above-ground process for removing contaminants from water or air. It involves contact between the water or air and activated carbon, which adsorbs the contaminants, usually by flowing the water or air through columns packed with carbon.
Carbonate - Any chemical containing the CO3= group; limestone and dolomite are examples of rocks formed primarily from carbonate minerals.
Catabolism - The biochemical processes involved in the breakdown of organic compounds, usually leading to the production of energy.
Catabolite repression - Repression of a variety of unrelated enzymes when cells are grown in a medium containing a specific substrate. See diauxy.
CERCLA - Comprehensive Environmental Response, Compensation and Liability Act (the first federal Superfund law).
Channeling - The short-circuit movement of water through a treatment train or vessel that severely diminishes its overall treatment efficiency.
Chelant - see complexing agent.
Chemotaxis - The movement of an organism in response to a chemical stimulus.
Chlorinated solvent - A hydrocarbon in which chlorine atoms substitute for one or more hydrogen atoms in the compound's structure. Chlorinated solvents commonly are used for grease removal in manufacturing, dry cleaning, and other operations. Examples include trichlorethylene (TCE), tetrachloroethylene (PCE), and trichloroethane.
Clarification - A step in wastewater treatment in which floc, grit, and entrained solids are removed by gravity. Solids are settled to the bottom of a clarifier and clear water flows up and out through skimmers or launders.
Clone - A population of cells all descended from a single cell; a number of copies of a DNA fragment obtained by allowing an inserted DNA fragment to be replicated by a phage or plasmid.
COD - Chemical oxygen demand; a test of the amount of oxygen needed for the complete non-biological oxidation of a sample.
Coenzyme - A low-molecular-weight chemical which participates in an enzymatic reaction by accepting and donating electrons or functional groups. Examples: NAD+, FAD.
Cometabolism - A reaction in which microbes transform a contaminant even though the contaminant cannot serve as an energy source for the organisms. To degrade the contaminant, the microbes require the presence of other compounds (primary substrates) that can support their growth.
Compatible solutes - Organic compounds that serve as cytoplasmic solutes to balance water relations for cells growing in environments of high salt or sugar.
Complementary - Nucleic acid sequences that can base pair with each other.
Complexing agent - A chemical agent that chemically bonds with a positively charged molecule, such as a metal. Complexing agents can be used to dissolve precipitated metals. synonym = chelant.
Conservative tracer - A chemical that does not undergo microbiological reactions but has transport properties similar to those of microbiologically reactive chemicals (such as the contaminant and oxygen).
Consortium - A group of different populations of microorganisms in close association that form a community structure with a certain symbiosis of inter-relationship in which each population contributes to the overall welfare of the group.
Constitutive enzymes - Enzymes(s) always produced by a cell regardless of the nature of the medium. An inducer compound is not required for the enzymes(s) formation.
CWA - Clean Water Act.
Cytoplasm - The aqueous material within a living cell.
D:
Dechlorinate - The removal of chlorine atoms from a compound.
Desorption - Opposite of sorption; the dissolution of chemicals from solid surfaces.
Deuterium - Hydrogen isotope with twice the mass of ordinary hydrogen; it contains one proton and one neutron in its nucleus.
Diatomaceous earth (DE) - comes from a mineral deposit of the calcareous skeletons of marine plankton (diatoms) that formed sediments in ancient oceans. The mineral is a finely divided powder and serves as an excellent filter aid and can act as a foundation for microbial attachment and growth in bioreactors.
Diauxy - Selective biodegradation of some organic compounds over others, which sometimes occurs when the compounds are present in mixtures.
Dispersion - The spreading and dilution of a solute front as it moves in the ground water (also called hydrodynamic dispersion). The spreading phenomenon occurs because of mechanical mixing during fluid advection (known as mechanical or hydraulic dispersion) and because of molecular diffusion due to the thermal-kinetic energy of the solute particles. Spreading of the solute in the direction of bulk flow is known as longitudinal dispersion. Spreading in directions perpendicular to the flow is called transverse dispersion. Longitudinal dispersion is usually much stronger than transverse dispersion.
DNA (deoxyribonucleic acid) - Substance within a cell that passes hereditary information from one generation to the next. A polymer of nucleotides connected via a phosphate-deoxyribose sugar backbone.
DNAPL - A NAPL more dense than water (see NAPL).
Domain - The highest level of biological classification, superseding kingdoms. The three domains of biological organisms are the Bacteria, the Archaea, and the Eukarya. Also used to describe a region of a protein having a distinct function.
E:
ECD - Electron-Capture Detector. A very useful detector for GC separations of halogenated organic compounds (see gas chromatograph). Also used for O, P, S, and
--NO2 containing compounds. Very weak response to ethers and hydrocarbons.
Electron - A negatively charged subatomic particle that may be transferred between chemical species in chemical reactions. Every chemical molecule contains electrons and protons (positively charged particles).
Electron acceptor - Compound that receives electrons (and therefore is reduced) in the energy-producing oxidation-reduction reactions that are essential for the growth of microorganisms and bioremediation. Common electron acceptors in bioremediation are oxygen, nitrate, sulfate, and iron.
Electron donor - Compound that donates electrons (and therefore is oxidized) in the energy-producing oxidation-reduction reactions that are essential for the growth of microorganisms and bioremediation. In bioremediation the organic contaminant often serves as an electron donor.
Engineered bioremediation - Type of bioremediation that stimulates the growth and biodegradative activity of microorganisms by adding nutrients, electron acceptors, or other stimulants to the site using an engineered system.
Enrichment culture - Use of selective culture media and incubation conditions to isolate microorganisms directly from nature.
Enzyme - Any of a vast number of biochemicals (usually proteins) produced by living organisms to use in transforming a specific compound. The enzyme serves as a catalyst in the compound's biochemical transformation.
Enzyme induction - Process whereby an organism synthesizes an enzyme in response to exposure to a specific chemical or other environmental inducers (e.g. heat, pressure, osmotic pressure).
Equilibrium - Condition in which a reaction has occurred to its maximum extent.
Estuarine - A coastal or near-shore environment characterized by waters of salinity less than that of open ocean (< 3.5% salt). This occurs in bays and at mouths of rivers where ocean water is impacted by fresh water inflow.
Eukarya - The phylogenetic domain containing all eukaryotic organisms.
Eukaryote - A cell or organism having a unit membrane-bound (true) nucleus and usually other organnelles.
Ex situ - Latin term referring to the removal of a substance from its natural or original position.
Extreme halophile - An organism whose growth is dependent on large amounts (generally > 10%) of NaCl.
F:
Facultative - A qualifying adjective indicating that an organism is able to grow either in the presence or absence of an environmental factor (e.g. facultative aerobe).
Fermentation - Process whereby microorganisms use an organic compound as both electron donor and electron acceptor, converting the compounds to fermentation products such as organic acids, alcohols, hydrogen, and carbon dioxide.
FID - Flame Ionization Detector. A very sensitive and stable detector for GC separations of organic compounds (see gas chromatograph). It gives no response to many inorganic gases (e.g., CO2, H2O, CO, SO2, H2S, and NH3).
Fixation - Process whereby microorganisms obtain carbon for building new cells from inorganic carbon, usually carbon dioxide.
Free product recovery - Removal of residual pools of contaminants, such as gasoline floating on the water table, from the subsurface.
G:
Gas chromatograph - Instrument used to identify and quantify volatile chemicals in a sample by a gas phase separation technique. After being separated on the chromatographic column, sample components pass through a detector (e.g., see FID and ECD) that creates an electric signal proportional to the concentration of sample components in the carrier gas stream. Also referred to as a GC.
GC/MS - A highly sophisticated analytical instrument or procedure that combines a Gas Chromatograph with a Mass Spectrometer for precise identification of chemical compounds.
Gene - A unit of heredity; a segment of DNA specifying a particular protein or polypeptide chain, a tRNA, or rRNA.
Gene cloning - The isolation of a desired gene from one organism and its incorporation into a suitable vector for the production of large amounts of the gene.
Gene probe - One class of nucleic acid (DNA or RNA) probes. Gene probes are used to identify the presence of a particular gene (such as the gene responsible for a particular biodegradative reaction) in the cell's DNA.
Genetically engineered microorganism (GEM) - An organism whose genes have been specifically and selectively altered by humans. For example, researchers have used genetic engineering to give bacteria the capability to degrade hazardous chemicals that normally resist biodegradation.
Genome - The complete set of genes present in an organism.
Genotype - The precise genetic constitution of an organism. Compare with Phenotype.
Glacial outwash - Materials (typically sand and gravel) deposited during the melting of glaciers.
Gradient - The direction of ground water flow, see hydraulic gradient.
Gratuitous metabolism - Reactions involving enzymes having high substrate specificity with respect to catalytic function but low specificity with respect to substrate binding. Also known as fortuitous metabolism.
H:
Halobacteria - Bacteria able to grow only in hypersaline environments.
Halogenate - Replacement of one or more hydrogen atoms on a chemical compound with atoms of a halogen, such as chlorine, fluorine, or bromine.
Halotolerant - Organisms able to metabolize at higher salt concentrations, but not requiring them.
Heterotroph - Organisms which utilize organic food sources; chemoorganotrophs.
High-performance liquid chromatograph - Instrument used to identify and quantify contaminants in a sample.
Homoacetogens - Bacteria that produce acetate as sole product of sugar fermentation or from H2 + CO2.
Hydraulic conductivity - A measure of the rate at which water moves through a unit area of the subsurface under a unit hydraulic gradient. It is a function of the media and the fluid flowing through it.
Hydraulic gradient - Change in head (i.e., water pressure) per unit distance in a given direction, typically in the principal flow direction.
Hydrocarbon - A chemical composed of carbon and hydrogen in any of a wide variety of configurations. Petroleum products, as well as many synthetic industrial chemicals, contain many different hydrocarbons.
Hydrolysis - Cleavage of organic carbon bonds where water is used in the reaction.
Hydrophobic compound - A "water-fearing" compound, such as oil, that has low solubility in water and tends to form a separate phase.
Hydrostatic - Pressure exerted by a column of water, see hydraulic gradient.
Hypersaline - Solutions having elevated salt concentrations. Thalassic solutions are those having salts in proportions found in sea water. Athalassic solutions have salts in altered proportions to those in sea water.
I:
Immobilized enzyme - An enzyme attached to a solid support over which substrate is passed and is converted into product.
In situ - Latin term meaning "in place" - in the natural or original position.
In vitro - In glass, away from the living organism
In vivo - In the body, in a living organism.
Inducible enzymes - Enzymes produced by a cell in response to a specific compound, or environmental condition, which is referred to as the inducer.
Infiltration gallery - Engineered system used to deliver materials that stimulate microorganisms in the subsurface. Infiltration galleries typically consist of buried perforated pipes through which water containing the appropriate stimulating materials is pumped.
Inorganic compound - A chemical that is not based on covalent carbon bonds. Important examples are metals, nutrients such as nitrogen and phosphorous, minerals, and carbon dioxide.
Insertion sequence (IS elements) - The simplest type of transposable element. Has only genes involved in transposition.
Integration - The process by which a DNA molecule becomes incorporated into another genome.
Interspecies hydrogen transfer - The process in which organic matter is degraded anaerobically by the interaction of several groups of microorganisms in which H2 production and H2 consumption are closely coupled.
Intrinsic bioremediation - A type of in situ bioremediation that uses the innate capabilities of naturally occurring microbes to degrade contaminants without taking any engineering steps to enhance the process.
Intrinsic permeability - A measure of the relative ease with which a liquid will pass through a porous medium. Intrinsic permeability depends on the shape and size of the openings through which the liquid moves.
Isotope - Any of two or more species of an element in the periodic table with the same number of protons. Isotopes have nearly identical chemical properties but different atomic masses and physical properties. For example, the isotope carbon 12 has six protons and six neutrons, while the isotope carbon 13 has six protons and seven neutrons. Both have atomic number 6 (the number of protons), but carbon 13 is more massive than carbon 12 because it carries an extra neutron.
Isotope fractionation - Selective degradation by microorganisms of one isotopic form of a carbon (or inorganic) compound over another isotopic form. For example, microorganisms degrade the 12C isotopes of petroleum hydrocarbons more rapidly than the 13C isotopes.
K:
Kilobase (kb) - a 1000 base fragment of nucleic acid. A kilobase pair is a fragment containing 1000 base pairs.
Kinetics - Refers to the rate at which a reaction occurs.
L:
Land ban - The regulations under RCRA that restrict disposal of certain classes of waste in or on the land.
Land farming - Above-ground process used to stimulate microorganisms to degrade contaminants in soil. The process involves spreading out the soil, adding nutrients, and tilling.
Ligand - See complexing agent. Also, an unspecified organic chemical species.
Limiting Factor - That nutritional element or compound in least abundance without which metabolism cannot occur.
Line Snubber - Pressure damping device consisting of a back-pressure diaphragm for smoothing pulses and providing even distribution in a flow line. Used with a diaphragm or peristaltic pump.
Lithostatic - Pressure exerted by a rock column; overburden.
Lithotrophs - Organisms which utilize inorganic electron donors for energy and reducing power. Usually considered synonymous with chemolithotroph.
LNAPL - A NAPL less dense than water (see NAPL).
Load Capacity - A measure of soil compressive strength.
Lysis - Breaking up of the microbial cell and release of the cytoplasm; Bursting of the cell membrane.
M:
Mass spectrometer - Instrument used to identify the chemical structure of a compound. Usually, the chemicals in the compound are separated beforehand by chromatography.
Matrix - The natural material into which a pollutant or contaminant is introduced, spilled, or disposed. Usually taken to be the chemical environment created or found in soil or water at a remediation site.
Messenger RNA (mRNA) - An RNA molecule transcribed from DNA which contains the information to direct the synthesis of a particular protein (enzyme).
Metabolic Intermediate - A chemical produced by one step in a multistep biotransformation.
Metabolism - Internal cellular biochemical reactions necessary for the maintenance of life. Or, the chemical reactions in living cells that convert food sources to energy and new cell mass.
Methanogen - A prokaryote that produces methane. Because they thrive without oxygen, and are also extremely sensitive to oxygen, methanogens can be important microbial components in subsurface biotransformations, where oxygen is often absent.
Methanotroph - A prokaryote capable of utilizing methane as a substrate. Complete oxidation of methane to carbon dioxide occurs by aerobic degradation pathways.
Methylotroph - An organism capable of oxidizing organic compounds which do not contain carbon-carbon bonds; if able to oxidize CH4, also a methanotroph.
Micelle - An aggregate of molecules, such as surfactant molecules, that form a small region of nonaqueous phase within an otherwise aqueous matrix.
Microaerophilic - Requiring O2 but at a level lower than atmospheric.
Microbe - The shortened term for microorganism (see microorganism).
Microcosm - A laboratory vessel set up to resemble as closely as possible the conditions of a natural environment.
Microhabitat - The immediate environment in intimate contact with living microbes which may be different from the surrounding medium.
Micronutrient - A trace element essential in nutrition.
Microorganism - An organism of microscopic or submicroscopic size. Microorganisms can destroy contaminants by using them as "food sources" for their own growth and reproduction.
Mineralization - The complete degradation of an organic chemical to carbon dioxide, water, and possibly other inorganic compounds.
Mixed Waste - More properly, Radioactive Mixed Waste. A specific class of hazardous waste that comprises all mixtures of regulated radioactive elements with any of the RCRA hazardous wastes. The RCRA waste is regulated under EPA and the RAD waste comes under the NRC regulations.
Mixotroph - An organism able to assimilate organic compounds as carbon sources while using inorganic compounds as electron donors.
Morphology - Cellular shape, dimensions, and spacial arrangement.
Most-probable-number (MPN) technique - A statistical culture-based test for estimating the number of organisms of a specific physiological type within a sample.
Motile - Capable of locomotion. Microorganisms having exterior flagella or other means of self-propulsion.
MPN - Most Probable Number test for bacterial count.
Mutagen - An agent that induces mutation, such as radiation or certain chemicals.
Mutagenesis - Forces causing the process of genetic mutation.
Mutation - Any of a number of events which alter the physical sequence of paired DNA chains (nucleic acid, genetic material) within a microbial cell resulting in a stable change in genotype (Chromosome DNA sequence) passed on to subsequent generations.
N:
NAPL - See nonaqueous-phase liquid.
Niche - The position held by a species of organism within its community and defined by its food sources, its physical/chemical environment, and relationship to other organisms in the community. Competition results when two or more species vie for the same niche in a community of organisms.
Nonaqueous-phase liquid (NAPL) - A liquid solution that does not mix easily with water. Many common ground water contaminants, including chlorinated solvents and many petroleum products, enter the subsurface in nonaqueous-phase solutions.
Nucleic acid probe - A strand of nucleic acid which can be labeled and used to hybridize to a complementary molecule from a mixture of other nucleic acids. In clinical and environmental microbiology, short segments of unique sequence (oligonucleotide probes) are used as nucleic acid probes for identifying specific or general groups of microorganisms, directly in the environmental or clinical specimen (without the requirement for culturing).
Nucleotide - A monomeric unit of nucleic acid, consisting of a sugar, a phosphate, and a nitrogenous base.
O:
Oligonucleotide probe - See nucleic acid probe.
Oligotrophic - Describing a body of water in which nutrients are in low supply.
Organic compound - A compound built from carbon atoms, typically linked in chains or rings.
Organotroph - A microorganism capable of utilizing organic carbon sources as food.
OSHA - Occupational Safety and Health Administration (U.S.)
Osmotic - A pressure differential favoring liquid flow from areas of lesser concentration to areas of greater concentration of dissolved solids.
Oxidation - Transfer of electrons away from a compound, such as an organic contaminant. The oxidation can supply energy that microorganisms use for growth and reproduction. Often (but not always), oxidation results in the addition of an oxygen atom and/or the loss of a hydrogen atom.
P:
Pathogen - A disease causing microorganism.
PCB - Poly-chlorinated Biphenyl. A compound in common use for several years (banned production in 1979) that was developed and used for dielectric fluid in electrical switch gear and transformers, heat transfer fluid, and turbine lube.
Persistence - When a chemical fails to undergo biodegradation under a specified set of conditions. A chemical may be inherently biodegradable, yet persist in the environment. Compare to recalcitrant.
Petroleum hydrocarbon - A chemical derived from petroleum by various refining processes. Examples include gasoline, fuel oil, and a wide range of chemicals used in manufacturing and industry.
Phreatic Zone - The saturated soil zone below the water table.
Phylogeny - The ordering of species into higher taxa and the construction of evolutionary trees based on evolutionary (natural) relationships.
Piezometer - An extremely sensitive device which can measure subtle changes in air or water pressures in the subsurface.
Plasmid - A fragment of genetic material, generally circular, that can be passed from one microorganism to another. An accessory DNA element is not essential for growth and which has no extracellular form.
Pleomorphic - Capable of multiple shapes, morphologically plastic.
Plume - A zone of dissolved contaminants. A plume usually originates from the contaminant zone and extends for some distance in the direction of ground water flow.
Polishing - The last in a sequence of treatment steps just prior to discharge. The gross amount of contamination is removed ahead of the polishing step which produces a finished effluent that meets or exceed regulatory limits.
Polymerase chain reaction (PCR) - A method for amplifying DNA in vitro, involving the use of oligonucleotide primers complementary to nucleotide sequences in a target gene and the copying of the target sequences by the action of DNA polymerase.
Porosity - The total porosity is defined as the ratio between the volume of the voids and the total volume of a soil or rock. It is usually reported as a decimal fraction or percent. The effective porosity is the percent of the porous media that consists of interconnected pore spaces that contribute to the flow of air or water.
Powdered activated carbon treatment (PACT) - Biomass suspended and fixed to carbon particles in completely mixed reactor. Carbon particles serve as both substratum for microbial attachment and to adsorb organic material.
Primary substrates - The electron donor and electron acceptor that are essential to ensure the growth of microorganisms. These compounds can be viewed as analogous to the food and oxygen that are required for human growth and reproduction.
Primer - A molecule (usually an oligonucleotide) to which DNA polymerase can attach the first nucleotide during DNA replication.
Prokaryote - A cell or organism lacking a unit membrane-bound (true) nucleus and other organnelles. Usually having its DNA in a single circular molecule.
Protocol - A highly specific sampling or analytic procedure.
Protozoan - A single-cell eukaryotic organism that is larger than a bacterium and may feed on bacteria.
PSH - Phase-Separated Hydrocarbon.
Psychrophile - An organism able to grow at low temperatures and showing a growth temperature optimum of < 15o C.
Pump-and-treat system - Most commonly used type of system for cleaning up contaminated ground water. Pump-and-treat systems consist of a series of wells used to pump contaminated water to the surface and a surface treatment facility used to clean the extracted ground water.
Pure culture - A culture containing a single kind of microorganism.
R:
Radiotracer/Radiolabeling - For most bioremediation applications a radiotracer is a carbon compound that has been labeled with 14C (a radioactive isotope of carbon) for the purpose of tracing the degradation pathway of the labeled compound.
Rate-limiting material - Material whose concentration limits the rate at which a particular process can occur.
RCRA - Resource Conservation and Recovery Act.
Recalcitrant - Any organic compound that is inherently resistant to any degree of biodegradation.
Recombinant DNA - A DNA molecule containing DNA originating from two or more sources.
Reduction - Transfer of electrons to a compound, such as oxygen. It occurs when another compound is oxidized.
Reductive dehalogenation - A variation on biodegradation in which microbially catalyzed reactions cause the replacement of a halogen atom on an organic compound with a hydrogen atom. The reactions result in the net addition of two electrons to the organic compound.
Replication - Conversion of one double-stranded DNA molecule into two identical double-stranded DNA molecules.
Reporter gene - A tool used with genetically engineered microorganisms. When a reporter gene is incorporated into a microorganism's genetic material, it provides a signal when the organism is present and active, or when a specific metabolic pathway is expressed. An example is a gene that produces a protein that causes the microorganism to emit light.
Ribonucleic Acid (RNA) - A polymer of nucleotides connected via a phosphate-ribose backbone, involved in protein synthesis.
Ribosomal RNA (rRNA) - Types of RNA found in the ribosome; some participate actively in the process of protein synthesis.
Ribosome - A cytoplasmic particle composed of ribosomal RNA and protein, which is part of the protein-synthesizing machinery of the cell.
16S rRNA - A large polynucleotide (ca 1500 bases) which functions as a part of the small subunit of the ribosome of prokaryotes and from whose sequence evolutionary information can be obtained; eukaryotic counterpart, 18S rRNA. Also used as a target for oligonucleotide probes.
S:
SARA - Superfund Amendments and Reauthorization Act.
Saturated zone - Part of the subsurface that is beneath the water table and in which the pores are filled with water.
SDWA - Safe Drinking Water Act.
Secondary substrate - A chemical that can be transformed by microorganisms through secondary utilization (see secondary utilization).
Secondary utilization - General term for the transformation of contaminants by microorganisms when the transformation yields little or no benefit to the organisms.
Selection - The ecological process by which more successful organisms evolve as the result of advantageous mutations and competition. Natural selection among living organisms can be thought of an adjustment in a population to changing natural environments. As conditions change, so does the makeup of the population. Artificial selection is the intentional alteration of the environment in order to encourage those changes that suit a specific need, e.g., if a population rich in specific degraders is desired, then the environment can be altered by addition of the specific target compound, which will favor those organisms which can degrade that compound, assuming degradation confers a competitive advantage.
Siderophore - Highly specific ion chelating organic ligands produced by some bacteria.
SITE - Superfund Innovative Technology Evaluation Program.
Slurry wall - A clay barrier constructed in the subsurface to prevent the spread of contaminants by preventing water flow.
Soil vapor extraction - See vapor recovery.
Sorption - Collection of a substance of the surface of a solid by physical or chemical attraction.
Substrate - A compound that microorganisms can use in the chemical reactions catalyzed by their enzymes.
Sulfate-reducer - A microorganism that converts sulfate to hydrogen sulfide. Because they can act without oxygen, sulfate-reducing bacteria can be important players in the oxygen-limited subsurface.
Surfactant - Soap or a similar substance that has a hydrophobic and a hydrophilic end. Surfactants can bond to oil and other immiscible compounds to aid their transport in water. Some microorganisms are active in production of surfactants, increasing the bioavailability of hydrophobic substances used as substrates.
SVE - Soil Vapor Extraction system for in situ removal of volatile chemical contamination in unsaturated soils.
Symbiosis - A relationship between two organisms.
Syntrophy - A nutritional situation in which two or more organisms combine their metabolic capabilities to catabolize a substance not capable of being catabolized by either one alone.
T:
Thermophile - A microorganism capable of growth at elevated temperatures.
TCLP - Toxic Characteristic Leaching Procedure (EPA). The testing procedure for RCRA toxic waste characteristic.
TOC - Total organic carbon test.
TPH - Total extractable Petroleum Hydrocarbons test performed by EPA Protocol 418.1.
Translation - The synthesis of protein using the genetic information in a messenger RNA as a template.
Transmissivity - A description of the capacity of an aquifer to transmit water. Equals the product of the aquifer thickness and the hydraulic conductivity.
Transport - Any movement of a fluid or particle within or through a geologic formation.
Transposable element - A genetic element that has the ability to move (transpose) from one site on a chromosome to another.
Transposon - A type of transposable element which, in addition to genes involved in transposition, carries other genes; often genes conferring selectable phenotypes such as antibiotic and metal resistance or catabolism of rarely encountered substrates, e.g. polyaromatic hydrocarbons.
U:
Unavailability - Situation in which a contaminant is sequestered from the microorganism, inhibiting the organism's ability to degrade the contaminant.
Unsaturated zone - Soil above the water table, where pores are partially or largely filled with air.
V:
Vadose zone - See unsaturated zone.
Vapor recovery - A method for removing volatile contaminants from the soil above the water table by circulating air through the soil.
Viability - That quality of organisms that allows them to grow and multiply and overcome environmental constraints.
Volatilization - Transfer of a chemical from the liquid to the gas phase (as in evaporation).
W:
Water table - Roughly speaking, this is the boundary between the unsaturated zone and the saturated zone of a unconfined aquifer. More specifically, it is the surface on which the fluid pressure in the pores of a porous medium is exactly atmospheric. In a shallow aquifer this is the level to which water will rise in a dug well under atmospheric conditions.
X:
Xenobiotic - Generally, a manmade chemical, or one that does not occur in nature as a result of biological activity.