aquifer - an underground formation saturated with water. For more info, see aquifer page.

bacterium - (plural = bacteria) a microorganism lacking a nucleus and genetically distinct from plants, animals, fungi and protists.

bioaugmentation - the addition of nonnative microbes to site to clean up toxic wastes.

biocurtain - a series of closely spaced wells spanning a aquifer (like a curtain spans a window) designed to intercept polluted water with an colonized zone of biodegrading microbes.

bioremediation - the addition of microbes to clean up toxic wastes.

brownfields - abandoned, idled, or under used industrial and commercial facilities where expansion or redevelopment is complicated by real or perceived environmental contamination. Brownfields can be located in urban, suburban, and rural areas. (Kirk's definition)

bug - in microbiologist's lexicon, an affectionate name for microorganism. Bug in this sense is not to be confused with beetles and their ilk.

carbon tetrachloride (CCl₄) - a hazardous compound used in manufacturing, cleaning and fumigation. The regulatory limit of carbon tetrachloride is 5 parts per billion (ppb). For more info, see carbon tetrachloride page.

carbon dioxide (CO₂) - a relatively inert gas which forms as a breakdown product of combustion, respiration, and CT degradation..

denitrifier - a bacterium capable of respiring (breathing) nitrate (NO₃-) or nitrite (NO₂-) instead of oxygen as an electron acceptor.

DNA probe - a small segment of DNA labeled with a visible marker used to detect the presence of a particular type of organism by selective hybridization to a known, specific DNA sequence in that organism..

enrichment (also known as "selective enrichment") - selection for particular organisms that can grow under given selective conditions.

formate - one of the products of carbon tetrachloride degradation by P. stutzeri strain KC.

iron chelator - a compound that reversibly binds onto iron (see siderophore).

microbe - short for microorganism. A generic term for any organism that completes its life cycle at a size too tiny to be seen with the naked eye (less than 1 millimeter).

microcosm - a small lab setup used to simulate conditions of a particular environment.

niche adjustment - a term coined to describe altering an environment to favor the growth of certain organisms.

nitrate - NO₃ - a common form of nitrogen used for fertilizer; a terminal electron acceptor for denitrifiers.

permeameter - device used to measure the permeability of soil, or in this case, aquifer material. The permeability of soil can predict the flow of material through the soil or aquifer.

pH - measure of hydrogen ions in solution. At higher pH, there are fewer hydrogen ions. pH affects biological and chemical processes. For example, less iron is soluble in water at high pH .

polymerase chain reaction (PCR) - PCR is a technique for creating millions of copies of a specific region of DNA. Two short DNA "primers" adhere to sites flanking the DNA segment of interest. DNA polymerase added to the reaction mixture amplifies the DNA between the primers.

pump and treat - conventional system of cleaning polluted aquifers by pumping out water, stripping the pollutant using non-biological methods such as air stripping or chemical treatment, and returning water to the aquifer.

Pseudomonas - a genus of Gram negative bacteria. Many pseudomonads are capable of degrading a variety of compounds.

pyridine-2,6-bis (thiocarboxylate) (PDTC) - a biomolecule produced by Pseudomonas stutzeri KC.

restriction enzymes - enzymes that cut DNA molecules at specific nucleotide sequences depending on the particular enzyme used. DNA molecules from different organisms may be cut up into pieces of unique sizes which may be seen by separating these pieces by gel electrophoresis. Enzyme recognition sites are usually 4 to 6 base pairs in length. Generally, the shorter the recognition sequence, the greater the number of fragments generated.

restriction fragment length polymorphism (RFLP) - a technique in which organisms may be differentiated by analysis of patterns derived from cleavage of their DNA. If two organisms differ in the distance between sites of cleavage of a particular restriction endonuclease, the length of the fragments produced will differ when the DNA is digested with a restriction enzyme. For example, DNA from P. stutzeri KC has a unique RFLP pattern that differentiates it from other isolates in the aquifer.

terminal restriction fragment length polymorphism (tRFLP) - a method to determine the diversity of genes in a particular community of organisms. In tRFLP the target gene is amplified from the community using standard PCR techniques with a 5' fluorescently tagged primer. The amplification products are digested with a restriction endonuclease and run on an automated sequencer. Because only the restriction fragment proximal to the labeled primer carries the flourescine, only this fragment is detected by the automated system. In general, each population of the community contributes a terminal fragment of one size. (definition from the Center for Microbial Ecology's tRFLP page at: http://www.cme.msu.edu/CME/RES_PROG/T_RFLP.html

siderophore - an extracellular biomolecule that grabs onto iron and making it more available to the bacterium that produces it (and sometimes other bacteria as well).

sorption - the process in which chemicals become associated with solid phases. Adsorption is sorption onto a 2-dimensional surface while absorption is sorption into a three-dimensional matrix.

sorption coefficient - the rate at which chemicals adhere to solids. For example, the more carbon tetrachloride adheres to sand particles in the aquifer the greater the sorption coefficient.