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Bioremediation and Phytoremediation Glossary

This is a glossary terms related to bioremediation (biological treatment) and phytoremediation (remediation using green plants) of environmental pollutants. Links to other environmental glossaries are at the bottom of the page.

Copyright 1998

 ABIOTIC: Not biotic or living.
 ACIDOPHILE: Organism that grows best under acid conditions 
 (down to a pH of 1).
 ADAPTATION: Change in an organism or population of organisms 
 through which they become more suited to the prevailing 
 environment.  Adaptation can be genetic and/or physiological. 
 AEROBE: An organism that can grow in the presence of air.
 AEROBIC: An environment that has a partial pressure of oxygen 
 similar to normal atmospheric conditions.
 ALKALOPHILE: Organism that grows best under alkaline conditions 
 (up to a pH of 10.5).
 ANAEROBIC: An environment without oxygen.
 ANAEROBE: An organism that grows in the absence of oxygen or air.
 ANAEROBIC RESPIRATION: (In some bacteria) Use of inorganic electron 
 acceptors other than oxygen as terminal electron acceptors for 
 energy yielding oxidative metabolism. NITRATE RESPIRATION is an 
 example of anaerobic respiration.
 ANOXIC: Literally "without oxygen." An adjective describing a 
 habitat devoid of oxygen.
 ANTHROPOGENIC: Derived from human activities. 
 AUTOTROPH: An organism that uses carbon dioxide as its source of 
 carbon for growth.  (Compare with HETEROTROPH.)
 BACTERIA: A group of diverse and ubiquitous prokaryotic 
 single-celled microorganisms.
 BIOACCUMULATION: Intracellular accumulation of environmental 
 pollutants such as heavy metals by living organisms.  
 BIOAUGMENTATION: The addition to the environment of microorganisms 
 that can metabolize and grow on specific organic compounds.
 BIOAVAILABILITY: The availability of chemicals to potentially 
 biodegradative microorganisms.
 BIOCHEMICAL OXYGEN DEMAND: (BOD) The requirement for molecular 
 oxygen by microbes during oxidation of biological substances in 
 sewage.  The BOD test measures the oxygen consumed (in mg/L) 
 over 5 days at 20 degrees C.
 BIODEGRADATION: The breakdown of organic substances by microorganisms.
 BIOFILTER: Apparatus that biodegrades volatile organic compounds in 
 air by passing the air through media containing biodegrading microbes.
 BIOMASS: The amount of living matter present in a particular habitat.
 BIOREMEDIATION: The process by which living organisms act to degrade 
 or transform hazardous organic contaminants.
 BIOSTIMULATION:  A process that increases activity of microorganisms 
 biodegrading contaminants.  For example, addition of nutrients, 
 oxygen, or other electron donors and acceptors.
 BIOTIC: Living.
 BIOTRANSFORMATION: Alteration of the structure of a compound by a 
 living organism or enzyme.
 BIOVENTING: The process of supplying oxygen in situ to oxygen 
 deprived soil microbes by forcing air through unsaturated 
 contaminated soil at low flow rates.  This stimulates biodegradation 
 and minimizes stripping volatiles into the atmosphere.  Frequently 
 used to remediate soil under structures since it is relatively 
 BROWNFIELD: An abandoned, idled, or under-used industrial or 
 commercial facility where expansion or redevelopment is complicated 
 by a real or perceived environmental contamination.
 BTEX: Benzene, toluene, ethylbenzene, and xylenes.
 CHEMICAL OXYGEN DEMAND: The amount of oxygen in milligrams per liter 
 to oxidize both organic and oxidizable inorganic compounds.
 COMETABOLISM: The biodegradation of a pollutant by an organism while 
 using some other compound(s) for growth and energy.  There is little 
 or no benefit to the biodegrading organism, the pollutant just 
 happens to be affected by the growth of the cometabolizing organism.
 CONSORTIUM: Two or more members of a natural assemblage in which each 
 organism benefits from the other. The group may collectively carryout 
 some process that no single member can accomplish on its own.
 CREOSOTE: An antifungal wood preservative used frequently to treat 
 telephone poles and railroad ties.  Creosote consists of coal tar 
 distillation products, including PHENOLS and PAHs.
 DCE: Dichloroethylene.
 DENITRIFICATION: The formation of gaseous nitrogen and/or oxides of 
 nitrogen from nitrate or nitrite by some bacteria during ANAEROBIC 
 RESPIRATION.  Denitrification only occurs in ANAEROBIC or 
 MICROAEROPHILIC conditions.  It can sometimes be used to remove 
 nitrate or nitrite from liquid wastes.
 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.
 contaminants near plant roots where compounds exuded by the roots 
 increase microbial biodegradation activity.  Other plant processes 
 such as water uptake by the plant roots can enhance biodegradation 
 by drawing contaminants to the root zone.
 ENRICHMENT: Culture in a liquid medium that results in the increase 
 of the population of an organism relative to others.  The liquid 
 culture frequently contains substances that encourage the growth of 
 the selected organism (Such as the chemical pollutant and mineral 
 ENZYMES: Proteins that act as biological catalysts.
 EUTROPHICATION: The enrichment of natural waters with inorganic 
 material especially nitrogen and phosphorous such that they support 
 excessive growth of plants and algae.  (Compare with OLIGOTROPHIC.)
 EX SITU: Out of the original position (Excavated).
 FACULTATIVE ORGANISM: Organism that can carry out both options of a 
 mutually exclusive process
 (e.g., aerobic and anaerobic metabolism).
 FERMENTATION: An energy yielding metabolism that involves a series 
 of oxidation-reduction reactions in which the substrate and terminal 
 electron acceptor are organic compounds.  Fermentation occurs in a 
 wide variety of bacteria and fungi.
 FUNGI: A group of diverse and widespread unicellular and 
 multicellular eukaryotic organisms.  Some species are important 
 in the decomposition of plant litter.
 HALOPHILIC: Organisms whose requirement for salt exceeds that of 
 other organisms.
 HETEROTROPH: Any organism that requires exogenous organic material 
 for growth and reproduction.
 IN SITU: In place, without excavation.
 INOCULUM: Material used to introduce a microorganism into a suitable 
 situation for growth. 
 ISOENZYME: An enzyme that occurs in more than one form in a given 
 species.  Sometimes called an isozyme.
 LIGNIN: A complex polymer that occurs in woody material of higher 
 plants.  It is highly resistant to chemical and enzymatic 
 degradation.  The WHITE ROT FUNGI are known for their lignin 
 degrading capability.
 MEDIUM: Any material that supports growth of an organism.
 MESOPHILE: An organism whose optimum growth range is 20-45 degrees C.  
 METHANOTROPH: Aerobic bacteria that can use methane as a sole source 
 of carbon.
 METHANOGEN: Bacteria that anaerobicly oxidize hydrogen to methane 
 and water using carbon dioxide as the electron acceptor.  These 
 occur in anaerobic muds, ponds, and sewage sludge. 
 MICROAEROPHILIC: An environment that is low in oxygen but is not 
 MICROBE: microorganism.
 MICROCOSM: A community or other unit that is representative of a 
 larger unity. 
 MICROFLORA: All of the microorganisms associated with location or 
 MICRONUTRIENT: Chemical element necessary for growth found in small 
 amounts, usually < 100 mg kg-1 in a plant. These elements consist of 
 B, Cl, Cu, Fe, Mn, Mo, and Zn.
 MICROORGANISMS: Includes bacteria, algae, fungi, and viruses.
 MINERALIZATION: The breakdown of organic matter to inorganic 
 materials (such as carbon dioxide and water) by bacteria and fungi.
 MINIMAL MEDIUM: Culture medium that lacks certain growth factors 
 so that it will support growth of only certain types of 
 microorganisms (These are often used for ENRICHMENT CULTURES).
 MOST PROBABLE NUMBER: A method for estimating the concentration of 
 microorganisms in a sample.  A given volume of liquid or suspension 
 is inoculated into each of (typically) 5 tubes containing growth 
 media.  Decreasing volumes are inoculated into successive sets of 
 5 tubes.  After an incubation period the tubes are scored for 
 growth or lack of growth.  Those tubes in which growth occurred 
 are assumed to have contained at least one VIABLE organism in the 
 inoculant.  The concentration of VIABLE microorganisms in the 
 original liquid or suspension is calculated using a statistical 
 MYCELIUM: (plural, mycelia)- Mass of hyphae that form the vegetative 
 body of many fungal organisms.
 MYCOBACTERIUM: A genus of aerobic bacteria found in soil and water 
 that are capable of biodegrading multi-ring compounds such as PAHs.
 MYCORRHIZA: A mutually beneficial association between a fungus and 
 the root of a plant.  These occur in a wide range of plants 
 including trees, shrubs, and herbaceous plants.     
 NAPL: Non-aqueous phase liquid.  This can be lighter than water 
 (LNAPL), or more dense than water (DNAPL).
 NITRATE RESPIRATION: (dissimilatory nitrate reduction)  The use of 
 nitrate as a terminal electron acceptor for ANAEROBIC RESPIRATION.  
 This process occurs under ANAEROBIC or MICROAEROPHILIC conditions.  
 Not all bacteria are capable of this form of metabolism and the 
 nitrate may not be reduced completely to nitrogen gas (stopping at 
 nitrite, for example).  When the nitrate is reduced to gaseous 
 forms the process is called DENITRIFICATION.  This can sometimes 
 be used to remove nitrate or nitrite from liquid wastes.
 NITRIFICATION: The oxidation of ammonia to nitrite and then nitrate 
 by bacterial species such as Nitrosomonas and Nitrobacter, 
 respectively.  This process is strictly aerobic.
 OBLIGATE: Any state or condition that is an essential attribute of 
 a given organism.  For example an obligate AEROBE can grow only 
 under aerobic conditions.
 OLIGOTROPHIC: Bodies of water poor in those nutrients that support 
 growth of aerobic photosynthetic organisms.  (Compare with 
 ORGANIC PUMP: Uptake of large quantities of water by plant (trees) 
 roots and translocation into the atmosphere to reduce a flow of 
 water. Used to keep contaminated groundwater from reaching a body 
 of water, or to keep surface water from seeping into a capped 
 landfill and forming leachate.
 OXIDASE: An enzyme that catalyses a reaction in which electrons are 
 removed from a substrate and donated directly to molecular oxygen.  
 OXYGENASE: An enzyme that catalyses a reaction in which one 
 (monooxygenase) or both (dioxygenase) atoms of molecular oxygen 
 are incorporated into a molecule of substrate.  Oxygenases 
 catalyze the first step in degradation of strait-chained and 
 aromatic hydrocarbons.
 PATHOGEN:  An organism capable of causing disease.
 PAH: Polynuclear aromatic hydrocarbon.  Multi-ring compounds found 
 in fuels, oils, and CREOSOTE.  These are also common combustion 
 PCBs: Polychlorinated biphenyls.
 PCE: (Perchloroethylene): Tetrachloroethylene.
 PCP: Pentachlorophenol.
 PHENOL: Carbolic acid (C6H5OH).  Phenols and substituted phenols 
 are used as antimicrobial agents in high concentrations.
 PHYTODEGRADATION: A process in which plants are able to degrade 
 (break down) organic pollutants through their metabolic processes.
 PHYTOEXTRACTION: Use of plants to extract contaminants (such as 
 metals) from the environment (especially soil). When the plants 
 are saturated with contaminants they are harvested.
 PHYTOMINING: Use of plants to extract inorganic substances of 
 economic value (precious metals, etc.)
 PHYTOREMEDIATION: Use of plants to remediate contaminated soil or 
 PHYTOSTABILIZATION: Use of soil amendments and plants to reduce 
 bioavailability and offsite migration of contaminants.
 PHYTOVOLATILIZATION: Use of plants to volatilize contaminants 
 (solvents, etc.) from soil or water.
 PLASMID:  Extra DNA in a cell that is usually dispensable, but may 
 confer an advantage to the cell, such as the ability to biodegrade 
 certain compounds or resistance to antibiotics.
 PSYCHROPHILE: An organism with an optimum growth temperature less 
 than 20 degrees C. 
 RECALCITRANT: Resistant to biodegradation.
 REDOX POTENTIAL: The oxidation-reduction potential of an environment.  
 Measures the tendency of the environment to be reducing 
 (donate electrons) or oxidizing (accept electrons).
 REDUCTIVE DECHLORINATION: Removal of Cl as Cl- from an organic 
 compound by reducing the
 carbon atom from C-Cl to C-H.
 RESPIRATION: Energy yielding metabolism in which oxygen is the 
 terminal electron acceptor for substrate oxidation.
 RHIZOFILTRATION: Uptake of contaminants by the roots of plants 
 immersed in water.  When the roots are saturated with contaminants 
 they are harvested.
 RHIZOPLANE: The surface of plant roots.
 RHIZOSPHERE: Soil in the area surrounding plant roots that is 
 influenced by the plant root.  Typically a few millimeters or at 
 most centimeters from the plant root.  Important because this area 
 is higher in nutrients and thus has a higher and more active 
 microbial population.
 SIDEROCHROMES: Compounds produced by microorganisms that are 
 involved with the uptake of iron by those microorganisms.
 SIDEROPHORES: See siderochromes.
 SPORES: (bacterial endospores) A metabolically dormant state of 
 bacteria in which they are more resistant to heat, chemicals, etc.  
 (Compare with VEGETATIVE.)
 SURFACTANT: A natural or synthetic chemical that promotes the 
 wetting, solubilization, and emulsification of various types of 
 organic chemicals.
 TCE: Trichloroethylene.
 THERMOPHILE: Any organism that has an optimum growth temperature 
 above 45 degrees C.
 TPH: Total petroleum hydrocarbons.
 VADOSE ZONE: Unsaturated zone of soil above the groundwater, 
 extending from the bottom of the capillary fringe all the way 
 to the soil surface.
 VC: Vinyl chloride.
 VEGETATIVE: Cells with an active metabolism.  Not dormant or SPORES.
 VIABLE: Living, or capable of growth.
 WILD TYPE-STRAIN: Strain of an organism isolated from nature. The 
 usual or native form of an organism as opposed to a mutant strain.
 WINOGRADSKY COLUMN: Glass column with an anaerobic lower zone and 
 an aerobic upper zone, which allows growth of microorganisms under 
 conditions similar to those found in nutrient-rich water and sediment.
 WEATHERING: All physical and chemical changes produced by 
 atmospheric agents.
 WHITE ROT FUNGI: Fungi that decompose all components of wood.  
 Important because they produce enzymes that are capable of acting 
 on and biodegrading a wide variety of compounds, including many 
 XENOBIOTIC: Compound foreign to biological systems. Often refers to 
 human-made compounds that are resistant or recalcitrant to 
 biodegradation and decomposition. 
 XEROPHILE: Organism adapted to grow at low water potential, i.e., 
 very dry habitats. 

A Few Good Links

Environmental Glossary: Extensive list of terms including many acronyms.
Water Quality Association Glossary of Terms: An excellent listing of water quality terms.
Air Quality Glossary: Lists terms related to air pollution including some acronyms and legal /regulatory definitions.
Glossary of Soil Microbiology Terms: In addition to soil microbiology terms there are many molecular biology, biochemical ,and some soil science terms.
Phytoremediation Bibliography: Over 800 citations that include peer reviewed journal articles, newspaper stories, presentations and posters from conferences, and book chapters.
Bioremediation Discussion Group Home Page: An e-mail discussion group. Check the excellent list of links, documents, and discussion archives. You can join the Group if you so desire.

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