F

facultative organism- Organism that can carry out both options of a mutually exclusive process (e.g., aerobic and anaerobic metabolism).

feedback inhibition- Inhibition by an end product of the biosynthetic pathway involved in its synthesis.

fermentation- Metabolic process in which organic compounds serve as both electron donors and electron acceptors.

fertilizer- Any organic or inorganic material of natural or synthetic origin (other than liming materials) added to a soil to supply one or more elements essential to plant growth.

field capacity- Content of water, on a mass or volume basis, remaining in a soil after being saturated with water and after free drainage is negligible.

filamentous- In the form of very long rods, many times longer than wide (for bacteria), in the form of long branching strands (for fungi).

fimbria (plural, fimbriae)- Short filamentous structure on a bacterial cell; although flagella-like in structure, generally present in many copies and not involved in motility. Plays a role in adherence to surfaces and in the formation of pellicles.

fission- Type of cell division in which overall cell growth is followed by formation of a crosswall which typically divides the fully grown cell into two similar or identical cells.

flagellate- protozoan that moves by means of one to several flagella.

flagellum (plural, flagella)- Whiplike tubular structure attached to a microbial cell responsible for motility.

fluorescent- Able to emit light of a certain wavelength when activated by light of a shorter wavelength.

fluorescent antibody- Antiserum conjugated with a fluorescent dye, such as fluorescein or rhodamine.

fluxes- Rate of emission, sorption, or deposition of a material from one pool to another. For example, the exchange of methane between the land and the atmosphere is a flux, while the production of methane within the soil is not.

food chain- Movement of nutrients from one life form to another as a result of the different feeding habits and dietary requirements of organisms in an ecosystem.

food web- Diagram of the interconnections of nutrient flow through a food chain.

free energy- Intrinsic energy contained in a given substance that is available to do work, particularly with respect to chemical transformations; designated D G.

fruiting body- Macroscopic reproductive structure produced by some fungi, such as mushrooms, and some bacteria, including myxobacteria. Fruiting bodies are distinctive in size, shape, and coloration for each species.

frustule- Siliceous wall and protoplast of a diatom.

fulvic acid- Yellow organic material that remains in solution after removal of humic acid by acidification.

fungistasis- Suppression of germination of fungal spores or other resting structures in natural soils as a result of competition for available nutrients, presence of inhibitory compounds, or both.

fungus (plural, fungi)- Nonphototrophic, eukaryotic microorganisms that contain rigid cell walls.

fusiform- Spindle-shaped; tapered at both ends.

G

gametangium- Fungal structure that contains one or more gametes.

gamete- In eukaryotes, the haploid cell analogous to sperm and egg, which results from meiosis.

gas chromatography- Chromatographic technique in which the stationary phase is a solid or an immobile liquid and the mobile phase is gaseous. The gaseous samples are separated based on their differential adsorption to the stationary phase.

gel- Inert polymer, usually made of agarose or polyacrylamide, that separates macromolecules such as nucleic acids or proteins during electrophoresis.

gene- Unit of heredity; a segment of DNA specifying a particular protein or polypeptide chain, a tRNA or an mRNA.

gene cloning- 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- A strand of nucleic acid which can be labeled and hybridized to a complementary molecule from a mixture of other nucleic acids.

genetic code- Information for the synthesis of proteins contained in the nucleotide sequence of a DNA molecule (or in certain viruses, of an RNA molecule).

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

genetic engineering- In vitro techniques for the isolation, manipulation, recombination, and expression of DNA.

genome- Complete set of genes present in an organism.

genotype- Precise genetic constitution of an organism.

genus (plural, genera)- The first name of the scientific name (binomial); the taxon between family and species.

Gibb's free energy- See free energy.

glycolysis- Reactions of the Embden-Meyerhof (glycolytic) pathway in which glucose is oxidized to pyruvate.

glycosidase- Enzyme that hydrolyzes a glucosidic linkage between two sugar molecules.

grazing- See predation.

Gram stain- Differential stain that divides bacteria into two groups, Gram-positive and Gram-negative, based on the ability to retain crystal violet when decolorized with an organic solvent such as ethanol. The cell wall of Gram-positive bacteria consists chiefly of peptidoglycan and lacks the outer membrane of Gram-negative cells.

gravitational water- Portion of total soil water potential due to differences in elevation.

groundwater- Portion of the water below the surface of the ground at a pressure equal to or greater than atmospheric.

growth- In microbiology, an increase in both cell number and cellular constituents.

growth factor- Organic compound necessary for growth because it is an essential cell component or precursor of such components and cannot be synthesized by the organism itself. Usually required in trace amounts.

growth rate- The rate at which growth occurs, usually expressed as the generation time.

growth rate constant- Slope of log10 of the number of cells per unit volume plotted against time.

growth yield coefficient- Quantity of biomass carbon formed per unit of substrate carbon consumed.

H

habitat- Place where an organism lives.

halogen- Any of the five elements F, Cl, Br, I, and At that form part of group VII A of the periodic table.

halophile- Organism requiring or tolerating a saline environment

haploid- In eukaryotes, an organism or cell containing one chromosome complement and the same number of chromosomes as the gametes.

heavy metals- Those metals which have densities > 5.0 Mg m-3. These include the metallic elements Cu, Fe, Mn, Mo, Co, Zn, Cd, Hg, Ni, and Pb. Al and Se have densities < 5 but are also considered heavy metals.

heterocyst- Differentiated cyanobacterial cell that carries out dinitrogen fixation.

heterokaryon- Hypha that contains at least two genetically dissimilar nuclei.

heterothallic- Hyphae that are incompatible with each other each requiring contact with another hypha of compatible mating type which, upon fusion, forms a dikaryon or a diploid.

heterotroph- Organism capable of deriving carbon and energy for growth and cell synthesis from organic compounds; generally also obtain energy and reducing power equivalents from organic compounds.

heterotrophic nitrification- Biochemical oxidation of ammonium to nitrite and nitrate by heterotrophic microorganisms.

holomorph- Whole fungus consisting of all sexual and asexual stages in its life cycle.

homokaryon- Fungal hypha in which all nuclei are genetically identical.

homothallic- Hyphae that are self-compatible in that sexual reproduction occurs in the same organism by meiosis and genetic recombination; fusion of hypha results in a dikaryon or diploid.

horizon- See soil horizon.

host- Organism capable of supporting the growth of a virus or other parasite.

humic acid- Dark-colored organic material extracted from soil by various reagents (e.g., dilute alkali) and that is precipitated by acid (pH 1 to 2).

humic substances- Series of relatively high-molecular-weight, brown-to-black substances formed by secondary synthesis reactions. The term is generic in a sense that it describes the colored material or its fractions obtained on the basis of solubility characteristics, such as humic acid or fulvic acid.

humification- Process whereby the carbon of organic residues is transformed and converted to humic substances through biochemical and chemical processes.

humus- Total of the organic compounds in soil exclusive of undecayed plant and animal tissues, their "partial decomposition" products, and the soil biomass. The term is often used synonymously with soil organic matter.

hybridization- Natural formation or artificial construction of a duplex nucleic acid molecule by complementary base pairing between two nucleic acid strands derived from different sources.

hygroscopic water- Water adsorbed by a dry soil from an atmosphere of high relative humidity.

hydrogen bond- Chemical bond between a hydrogen atom of one molecule and two unshared electrons of another molecule.

hydrogen- oxidizing bacterium-Facultative lithotrophs that, in the absence of an oxidizable organic source, oxidize H2 for energy and synthesize carbohydrates with carbon dioxide as their source of carbon.

hypha (plural, hyphae)- Long and often branched tubular filament that constitutes the vegetative body of many fungi and funguslike organisms. Bacteria of the order Actinomycetes also produce branched hyphae.

hymenium- Layer of hyphae which are fertile in producing asci (fungi in the phylum Ascomycota) or basidia (fungi in the phylum Basidiomycota) from the process of meiosis.

hyperparasite- Parasite that feeds on another parasite.

I

illuviation- Deposition of soil material removed from one horizon to another in the soil.

immobilization- Conversion of an element from the inorganic to the organic form in microbial or plant biomass.

immunity- The ability of a human or animal body to resist infection by microorganisms or their harmful products such as toxins.

immunoblot (western blot)- Detection of proteins immobilized on a filter by complementary reaction with specific antibody.

immunoglobulin- Antibody.

immunogen- Substance which is capable of eliciting immune response. An immunogen usually has a fairly high molecular weight (usually greater than 10,000), thus, a variety of macromolecules such as proteins, lipoprotein, polysaccharides, and some nucleic acids can act as immunogens.

immunofluorescence- Technique to visualize specific antibodies and any attached homologous antigens by means of conjugating the antibodies to a fluorescent dye.

inducible enzyme- Enzyme synthesized (induced) in response to the presence of an external substance (the inducer).

infection- Growth of an organism within another living organism.

infection thread- Cellulosic tube in a root hair through which rhizobia can travel to reach and infect root cells.

infrared (IR)- The portion of the electromagnetic spectrum with wavelengths from about 0.75 µm to 1 mm.

inhibition- Prevention of growth or function.

inoculate- To treat with microorganisms for the purpose of creating a favorable response. For example, treatment of legume seeds with rhizobia to stimulate N2 fixation.

inoculum- Material used to introduce a microorganism into a suitable situation for growth.

insertion- Genetic mutation in which one or more nucleotides are added to DNA.

insertion sequence (IS element)- Simplest type of transposable element. Has only genes involved in transposition.

integration- Process by which a DNA molecule becomes incorporated into another genome.

intracellular- Inside the cell.

in vitro- Literally "in glass"; it describes whatever happens in a test tube or other receptacle, as opposed to in vivo. When a study or an experiment is done outside the living organism, in test tube, it is done in vitro.

in vivo- In the body, in a living organism, as opposed to in vitro; when a study or an experiment is done in the living organism, it is done in vivo.

ions- Atoms, groups of atoms, or compounds, that are electrically charged as a result of the loss of electrons (cations) or the gain of electrons (anions).

irrigation- Intentional watering of the soil.

isoenzyme (isozyme)- When two different enzymes catalyze the same reaction(s), they are isoenzymes of each other. Isoenzymes could differ from each other in their primary structure or electrophoretic mobility.

isolation- Any procedure in which an organism present in a particular sample or environment, is obtained in pure culture.

isomorphous substitution - Substitution in a crystalline clay sheet of one atom by a similarly sized atom of lower valence.

isotope- Different form of the same element containing the same number of protons and electrons, but differing in the number of neutrons.