Environmental Remediation Sciences Program

General Information: Glossary

Abiotic Not biotic or living.
Accelerated bioremediation   Bioremediation within the subsurface at a given site that is accelerated beyond the normal actions of the naturally occurring microbial community and naturally occurring chemical and geological conditions.
Actinide Any element in the series of elements with atomic numbers in the range beginning with actinium (89) or thorium (90) and ending with lawrencium (103).
Advection The process by which solutes are transported by the bulk motion of the flowing groundwater.
Aerobic Living, active, or occurring only in the presence of oxygen.
Amensalism An interspecific interaction in which one species population is inhibited, typically by toxin produced by the other, which is unaffected.
Alcohol An organic chemical containing one or more hydroxyl groups (-OH). Alcohols can be liquids, semisolids, or solids at room temperature.
Aldehyde One of a class of organic compounds containing the CHO radical.
Anaerobic Living, active, or occurring in the absence of free oxygen.
Anion A negatively charged ion. The ion in an electrolyzed solution that migrates to the anode.
Antibody Any of the body globulins that combine specifically with antigens and neutralize toxins, agglutinate bacteria or cells, and precipitate soluble antigens.
Aquifer Water-bearing stratum of permeable rock, sand, or gravel.
Archaeobacteria A group of microorganisms that are only distantly related to eukaryotes and prokaryotes and comprise the domain Archaea.
Assessment   An appraisal or evaluation (e.g., assessment of the degree of success of a remediation procedure at a contamination site).
Autochthonous Indigenous, natural, aboriginal; formed or occurring in the place where found.
Bioaccumulation Intracellular accumulation of environmental pollutants such as heavy metals by living organisms, including microorganisms, plants, and humans.
Bioaugmentation The addition to the environment of bacteria or fungi that can metabolize and grow on specific organic compounds.
Bioavailability The availability of chemicals to potentially biodegradative microorganisms; the availability of a toxic chemical to cause an adverse effect in higher life forms (e.g., humans).
Bio-barrier A biologically active zone that is placed in the subsurface perpendicular to the normal flow of a contaminant plume so that the contaminant can be adsorbed and biologically degraded.
Bio-chelator A biochemical compound (synthesized by living organisms) that binds and forms complexes with trace elements and polyvalent cations.
Biocolloid A colloid or colloidal mixture of biological components (see Colloid).
Biodegradation The breakdown of organic substances by microorganisms.
Biogeochemical dynamics  The temporal behavior of coupled biological, hydrological, and geochemical processes in geologic media.
Biomass The amount of living matter present in a particular habitat, usually expressed as dry weight per unit area or volume or as weight per unit volume.
Biomolecular engineering  The application of engineering technology to the solution of problems pertaining to organic molecules occurring in living organisms, especially macromolecules.
Biopolymer Microbial products, either exopolysaccharides or polyhydroxyalkanoates, that can be manufactured commercially from renewable resources, are biodegradable, and provide alternatives to traditional plant and algal gums or to plastics made from hydrocarbons.
Bioreactor Vessel or tank in which whole cells or cell-free enzymes transform raw materials into biochemical products and/or less undesirable by-products.
Bioremediation The process by which living organisms act to degrade hazardous organic contaminants or transform hazardous inorganic contaminants to environmentally safe levels in soils, subsurface materials, water, sludges, and residues.
Biosequestration The conversion of a compound through biological processes to a form that is chemically or physically isolated.
Biostimulation Addition of nutrients, oxygen, or other electron donors and acceptors so as to increase the number of indigenous microorganisms available for degradation of contaminants. Generally, any process that will increase the rates of biological degradation.
Biosurfactant A surface-active agent produced by microorganisms (see Surfactant).
Biota The animal and plant life of a region.
Biotic Of or relating to life; induced or caused by the action of living beings.
Biotransformation   Alteration of the structure of a compound by a living organism or enzyme.
Cell-free extracts Components (e.g., enzymes and biochelators) produced in living systems (either plant or animal) that can be removed from those systems and then used in bioremedial activities.
Chelator An agent that causes formation of a chelate--a heterocyclic molecule in which a metal ion is bound to at least two nonmetal ions in the same molecule.
Chemotaxis   Movement of cells or organisms toward or away from chemical stimuli.
Chemotropism Orientation response of cells or organisms in relation to chemical stimuli.
Chromatography A process of separating gases, liquids, or solids in a mixture or solution by adsorption, as selective adsorption on clay, silica gel, alumina, or paper.
Colloid Any gas, solid, or liquid in a fine state of subdivision, with particles too small to be visible in an ordinary optical microscope, that is dispersed in a continuous gaseous, liquid, or solid medium and does not settle or settles very slowly.
Cometabolism Biotransformation of a compound by a microorganism that is incapable of using the compound as a source of energy or growth.
Commensalism A close and permanent association between two populations of organisms in which one population benefits without damaging or benefiting the other.
Community Assemblage of species (populations) of microorganisms that occur and interact within a given habitat
Community dynamics Temporal changes in the structure and function of a community.
Complexing agent A dissolved ligand that binds with a simple charged or uncharged molecular species in a liquid solution to form a complex chemical species.
Conjugation The transfer of genetic material, in particular the transfer of microbial genes or gene clusters, either between or within species.
Cytochrome Any of several respiratory pigments that occur in animal and plant cell membranes and serve to transfer electrons from a substrate to a terminal acceptor such as oxygen.
Dehalogenate To remove halogen (Cl, F, Br) atoms from a molecule.
Ecology The study of the relationships between living organisms and between organisms and their environment.
Ecotoxicity The quality, state, or relative degree of being toxic or poisonous to the environment and the ecological system.
Eh Standard oxidation-reduction potential (redox potential); the energy gained in the transfer of 1 mol of electrons from an oxidant to H2.
Electromagnetic Of, relating to, or produced by electromagnetism, magnetism developed by a current of electricity.
Electron acceptor Small inorganic or organic compound that is reduced to complete an electron transport chain. Compound that is reduced in a metabolic redox reaction.
Electron donor Small inorganic or organic compound that is oxidized to initiate an electron transport chain. Compound from which electrons are derived in a metabolic redox reaction.
ELISA Enzyme-linked immunosorbent assay based on enzyme-labeled immunoreactants for use in the detection of analytes in clinical specimens
Endogenous Growing from or on the inside. Developing within the cell. Constituting or relating to metabolism of the nitrogenous constituents of cells or tissues. Arising from internal structural or functional causes.
Energetics The physics of energy and its transformations.
Eubacteria Prokaryotes that are distinct from archaeobacteria (see their respective definitions).
Eukaryotes Organisms that maintain their genome within a defined nucleus. (Not used in any formal taxonomic system, but now may be used to refer to members of the domain Eucarya.)
Expression system A system in which a cloned gene can be expressed. Elements used to evaluate the quality of an expression system include the number of copies of the gene per cell, the strength of the transcriptional promoter, the presence of the bacterial ribosome binding site, codon usage, and the fate of the protein.
Extremophiles A group of organisms whose growth is dependent on extreme environmental conditions, e.g., extreme halophiles, extreme psychrophiles, extreme thermophiles.
Ex situ In a position or location other than the natural or original one.
Feedback inhibition Mechanism by which the end product of the cell's biosynthetic pathway inhibits the activity of the first enzymes in the same pathway. This mechanism controls enzymatic activity so that resources can be conserved and regulated.
Gene A section of DNA coding for a single polypeptide chain, a particular species of transfer or ribosomal RNA, or a sequence that is recognized by and interacts with regulatory proteins.
Genetic engineering The application of engineering technology to the isolation and study of single genes, and the reintroduction of these genes into cells of the same or different species.
Genome The sum of all chromosomal genes in a haploid cell (including prokaryotes and archaea), or the haploid set of chromosomes in a eukaryotic cell.
Genotype The type species of a genus. The genetic constitution of an individual or group. The totality of genes possessed by an individual or group.
Geohydrological Referring to the character, source, and mode of the occurrence and flow of underground water.
Geology The geologic features of an area. The science that deals with the history of the earth and its life, especially as recorded in the rocks.
Geomechanics A branch of geology that embraces the basic fundamentals of structural geology and a knowledge of the response of natural materials to deformation or changes due to the application of stress or strain energy.
Geophysical Of, relating to, or based on the physics of the earth, including the fields of meteorology, hydrology, oceanography, seismology, volcanology, magnetism, radioactivity, and geodesy.
Heavy metals Metallic elements with high molecular weights, generally toxic in low concentrations to plant and animal life. Such metals are often residual in the environment and exhibit biological accumulation. Examples include mercury, chromium, cadmium, arsenic, and lead.
Heterocyst One of three types of specialized cells that form in filamentous cyanobacteria in response to environmental conditions, involved in the fixation of atmospheric nitrogen.
Heterogeneity The quality or state of being heterogeneous, i.e., varying in space or time.
Heterologous Consisting of different elements or of like elements in different proportions.
Horizontal gene transfer An evolutionary event involving the transfer of genes, from one species to another, in which the viable offspring gain genetic diversity.
Hydrocarbons Strictly, any of a large class of organic compounds containing only carbon and hydrogen; often used to include substituted hydrocarbons (e.g., alcohols, chlorinated solvents).
Hydrology A science dealing with the properties, distribution, and circulation of water; the study of water on the surface of the land, in the soil and underlying rocks, and in the atmosphere, particularly with respect to evaporation and precipitation.
In situ In place; in the natural or original position or location.
Interfacial Included between two plane surfaces or faces. Relating to or situated at the boundary between two phases, such as liquid-liquid, liquid-solid, and gas-liquid interfaces.
Interlayer transfer The transfer of chemicals and living organisms over a distance between layers of mineral surfaces in soil.
Ketone Organic compound characterized by a carbonyl group attached to two carbon atoms, usually contained in hydrocarbon radicals or in a single bivalent radical, similar to an aldehyde but less reactive.
Kinetics A branch of science that focuses on the rates of biological, physical, or chemical changes.
Leaching The process or an instance of separating the soluble components from some material by percolation. The process or an instance of removing nutritive or harmful elements from soil by percolation.
Mass spectroscopy The measurement and interpretation of electromagnetic spectra generated when a beam of ions is sent through a combination of electric and magnetic fields such that the ions are deflected according to their masses. Used to determine the masses of atoms or molecules.
Mesocosm A field-scale model utilized to understand the interactive relationships between microbial populations and the roles played by microbial populations within ecosystems.
Methanogen A methane-producing archaeon.
Methanotroph A methane-oxidizing bacterium.
Microautoradiography The technique of obtaining photographic images of microscopic samples by using neutron, x, or gamma radiation emitted from the sample onto a photoemulsion.
Microbial ecology The field of study that examines the interactions of microorganisms with their biotic and abiotic surroundings.
Microbiology A branch of biology dealing especially with microscopic forms of life (bacteria, archaea, protozoa, algae, viruses, and fungi).
Microcosm A laboratory-scale model used to understand the interactive relationships between microbial populations and the roles played by microbial populations within ecosystems.
Microorganism Any organism of microscopic or ultramicroscopic size.
Mineralization The breakdown of organic materials into inorganic materials brought about by microorganisms.
Molecular biology A branch of biology dealing with the ultimate physicochemical organization of living matter at the molecular level.
Molecular evolution The divergence of genes in sequence as they evolve from a common ancestor. The evolution of genomes through such genetic mechanisms as mutation, recombination, and gene duplication.
Morphology A branch of biology that deals with the form and structure of microorganisms, animals, and plants. Alternately, the external structure of rocks in relation to the development of erosional forms or topographic features.
Mutualism A stable condition in which two organisms of different species live in close physical association, each organism deriving some benefit from the other.
Natural bioremediation Bioremediation at a given site as a function of the naturally occurring microbial population and naturally occurring chemical, biological, and geological conditions.
Parasitism A relationship in which an organism of one kind lives in, on, or in intimate association with an organism of another kind, at whose expense it obtains food and usually other benefits.
Pathway engineering The application of engineering technology to alter or construct a sequence of enzymatically catalyzed chemical reactions.
Percolation Gravity flow of groundwater through the pore spaces in rock or soil.
pH The negative logarithm of the effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per liter.
Phenotypic Of, relating to, or constituting a detectable expression of the interaction of genotype and the environment; the visible expression of genotype.
Photon A massless elementary particle that is the carrier of radiant energy (as light or x rays).
Phototropism A growth-mediated response of plants or microorganisms to stimulation by visible light.
Phototaxis The ability of bacteria to detect changes in light intensity and respond by moving away from or toward the light.
Phylogeny The evolutionary history of a group of organisms. The sign and evolution of higher taka; phylogenesis.
Phthalate A salt or ester of phthalic acid.
Physiochemical Of or relating to physiological chemistry, a branch of science dealing with the chemical aspects of physiological and biological systems.
Phytoremediation Remediation performed by plants.
Plume An elongated body of fluid, usually mobile and varying in shape.
Predation A mode of life in which food is primarily obtained by killing and consuming.
Prokaryotes Organisms that maintain their genome dispersed throughout the cytoplasm. (Not used in any formal taxonomic system, but previously used interchangeably with the term "bacteria.") More recently, one of three domains of life -- the Prokarya.
Promoter A substance that in very small amounts is able to increase the activity of a catalyst. A DNA sequence that directs RNA polymerase to bind and initiate, transcription of genes or operons.
Radionuclides Nuclides that emit radioactivity (alpha, beta, or gamma particles) or fission into smaller nuclides.
Random mutagenesis The random occurrence or induction of mutation.
Recalcitrant Resistant to microbial attack.
Redox reactions Reactions of oxidation and reduction.
Regulatory elements The relatively short nucleotide sequences in DNA that play important roles in controlling gene expression.
Respiration Any of various energy-yielding oxidative reactions in living matter that typically involve transfer of any substrate (organic or inorganic) to a terminal electron acceptor, usually oxygen.
Rhizosphere Soil that surrounds and is influenced by the roots of a plant.
Secondary metabolism   A metabolic process that produces a metabolite, which peaks only after the main growth phase of the cell is completed.
Sequence The succession of one thing or event after another, as of genes along a strand of DNA or geological events in time.
Soil matrix An assemblage of mineral particles of various sizes, shapes, and chemical characteristics, together with organic materials, in various stages of decomposition and living soil populations.
Spatial heterogeneity A condition or state that varies with position in space.
Sporulation The formation of spores by bacteria. Division of fungi into many small spores.
Stochastic Involving a random variable. Involving chance or probability.
Subsurface The geologic zone below the surface of the earth. Rock and soil materials lying near, but not exposed at, the Earth's surface.
Surfactant A natural or synthetic chemical that promotes the wetting, solubilization, and emulsification of various types of organic chemicals.
Synchrotron An apparatus for imparting very high speeds to charged particles by means of a high-frequency electric field and a low-frequency magnetic field.
Taxonomy Study of the characterization, classification, and naming of organisms according to standard rules. Most modern taxonomies are phylogenetic (or natural); they attempt to group organisms according to evolutionary descent.
Temporal heterogeneity A condition or state that changes in time.
Thermodynamics A branch of physics and physical chemistry that deals with the mechanical actions or relationships of heat.
Transduction The transfer of genetic determinants from one microorganism to another by means of a viral agent.
Transformation In microbiology, genetic transfer wherein DNA from a donor cell enters a recipient cell and is incorporated into the recipient DNA by genetic recombination.
Transposon A segment of DNA with a repeat of an insertion sequence element at each end and which can migrate from one plasmid to another within the same bacterium, to a bacterial chromosome, or to a bacteriophage.
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