D

decomposer- Heterotrophic organism that breaks down organic compounds.

decomposition- Chemical breakdown of a compound into simpler compounds, often accomplished by microbial metabolism.

defined medium- Medium whose exact chemical composition is quantitatively known.

degradation- Process whereby a compound is usually transformed into simpler compounds.

denaturation- Process where double-stranded DNA unwinds and dissociates into two single strands. The reverse of DNA-DNA hybridization.

denitrification- Reduction of nitrate or nitrite to molecular nitrogen or nitrogen oxides by microbial activity (dissimilatory nitrate reduction) or by chemical reactions involving nitrite (chemical denitrification).

deoxyribonucleic acid (DNA)- Polymer of nucleotides connected via a phosphate-deoxyribose sugar backbone; the genetic material of the cell.

derepressible enzyme- Enzyme that is produced in the absence of a specific inhibitory compound acting at the transcriptional level.

diatom- Alga with siliceous cell walls that persist as a skeleton after death. Any of the microscopic unicellular or colonial alga constituting the class Bacillariophyceae.

diatomaceous earth-Geologic deposit of fine, grayish siliceous material composed chiefly or wholly of the remains of diatoms. It may occur as a powder or as a porous, rigid material.

diazotroph- Organism that can use dinitrogen as its sole nitrogen source, i.e. capable of N2 fixation.

differential medium- Cultural medium with an indicator, such as a dye, which allows various chemical reactions to be distinguished during growth.

diffusion (nutrient)- Movement of nutrients in soil that results from a concentration gradient.

dikaryon- Two nuclei present in the same hyphal compartment; they constitute a homokaryon when both nuclei are genetically the same or a heterokaryon when each nucleus is genetically different from the other.

dilution plate count method- Method for estimating the viable numbers of microorganisms in a sample. The sample is diluted serially and then transferred to agar plates to permit growth and quantification of colony-forming units.

dinitrogen fixation- Conversion of molecular dinitrogen (N2) to ammonia and subsequently to organic combinations or to forms useful in biological processes.

diploid- In eukaryotes, an organism or cell with two chromosome complements, one derived from each haploid gamete.

direct count- Method of estimating the total number of microorganisms in a given mass of soil by direct microscopic examination.

disinfectant- Agent that kills microorganisms.

dissimilatory nitrate reduction- see denitrification.

dissimilatory nitrate reduction to ammonium (DNRA)-Use of nitrate by organisms as an alternate electron acceptor in the absence of oxygen resulting in the reduction of nitrate to ammonium.

DNA fingerprinting- Molecular genetic techniques to assess possible differences among DNA in a samples.

DNA library- Collection of cloned DNA fragments which in total contain genes from the entire genome of an organism; also called a gene library.

dolipore septum- Specialized crosswall separating compartments of a hypha of fungi in the phylum Basidiomycota; consisting of a central pore covered with perforated membranes on both sides (called a parenthosome).

domain- Highest level of biological classification, superseding kingdoms. The three domains of biological organisms are the Bacteria, the Archaea, and the Eukarya.

doubling time- Time needed for a population to double in number or biomass.

E

ecology- Science which studies the interrelations among organisms and between organisms and their environment.

ecosystem- Community of organisms and the environment in which they live.

Ectomycorrhiza (EM)- Mycorrhizal type in which the fungal mycelia extend inward, between root cortical cells, to form a network (Hartig net) and outward into the surrounding soil. Usually the fungal hyphae also form a mantle on the surface of the root.

edaphic- (i) Of or pertaining to the soil. (ii) Resulting from or influenced by factors inherent in the soil or other substrate, rather than by climatic factors.

Eh- Potential generated between an oxidation or reduction half-reaction and the H electrode in the standard state.

electron acceptor- Substance that accepts electrons during an oxidation-reduction reaction. An electron acceptor is an oxidant.

electron donor- Substance that donates electrons in an oxidation-reduction reaction. An electron donor is a reductant.

electron-transport chain- Final sequence of reactions in biological oxidations composed of a series of oxidizing agents arranged in order of increasing strength and terminating in oxygen.

electron- transport chain phosphorylation- See oxidative phosphorylation.

electrophilic compounds- Chemicals that attack or are drawn to regions in other chemicals in which electrons are readily available; oxidizing agents act as electrophilic compounds.

electrophoresis- Separation of charged molecules, such as nucleic acids, in an electrical field.

eluviation- Removal of soil material from a layer of soil as a suspension.

Embden-Meyerhof-Parnas pathway (Embden-Meyerhof pathway; EMP pathway)- A biochemical pathway that degrades glucose to pyruvate; the six-carbon stage converts glucose to fructose-1,6-bisphosphate, and the three-carbon stage produces ATP while changing glyceraldehyde-3-phosphate to pyruvate.

endergonic reaction- Chemical reaction that proceeds with the consumption of energy.

endomycorrhiza- Mycorrhizal association with intracellular penetration of the host root cortical cells by the fungus as well as outward extension into the surrounding soil.

endoenzyme- Enzyme that operates along the internal portions of a polymer.

endonuclease- Endoenzyme that cleaves phosphodiester bonds within a nucleic acid molecule.

endophyte- Organism growing within a plant. The association may be symbiotic or parasitic.

endospore- Differentiated cell formed within the cells of certain Gram-positive bacteria and extremely resistant to heat and other harmful agents.

enrichment culture- Technique in which environmental (including nutritional) conditions are controlled to favor the development of a specific organism or group of organisms.

enteric bacteria- General term for a group of bacteria that inhabit the intestinal tract of humans and other animals. Among this group are pathogenic bacteria such as Salmonella and Shigella.

enzyme- Protein within or derived from a living organism that functions as a catalyst to promote specific reactions.

enzyme-linked immunosorbent assay (ELISA)- Immunoassay that uses specific antibodies to detect antigens or antibodies. The antibody-containing complexes are visualized through an enzyme coupled to the antibody. Addition of substrate to the enzyme-antibody-antigen complex results in a colored product.

episome- Plasmid that replicates by inserting itself into the bacterial chromosome.

epitope- The region of an antigen to which the variable region of an antibody binds.

ericoid mycorrhiza- Type of mycorrhiza found on plants in the Ericales. The hyphae in the root are able to penetrate cortical cells (endomycorrhizal habit); however, no arbuscules are formed. Major forms are ericoid, arbutoid, and monotropoid.

Eubacteria- Old term for the Bacteria.

Eukarya- Phylogenetic domain containing all eukaryotic organisms.

eukaryote- Organism having a unit membrane-bound nucleus and usually other organelles.

eutrophic- Having high concentrations of nutrients optimal, or nearly so, for plant or animal growth. Can be applied to nutrient or soil solutions and bodies of water.

exergonic reaction- Chemical reaction that proceeds with the liberation of energy.

exponential growth- Period of sustained growth of a microorganism in which the cell number constantly doubles within a fixed time period.

exponential phase- Period during the growth cycle of a population in which growth increases at an exponential rate. As referred to as logarithmic phase.

exobiology- Branch of biology concerned with the effects of extraterrestrial environments on living organisms.

exoenzyme- Enzyme that acts at the end of a polymer cleaving off monomers and dimers and sometimes larger chain fragments.

extracellular- Outside the cell.

exudate- Low molecular weight metabolites that leak from plant roots into soil.