soil bio terms [glossary?]

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Soil Microbiology Terms
Compiled by David Sylvia - Last update: August 25, 1998
Primary sources for this glossary were the Glossary of Soil Science Terms and Glossary of Microbiology

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Alphabetical Breakdown of Glossary Terms
A , B, C , D , E, F , G , H , I , J thru M, N thru Q, R thru S, T thru Z

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A

absorption- Movement of ions and water into as organism as a result of metabolic processes, frequently against an electrochemical potential gradient (active) or as a result of diffusion along an activity gradient (passive).

acetogenic bacterium- Prokaryotic organism that uses carbonate as a terminal electron acceptor and produces acetic acid as a waste product.

acetylene-block assay- Estimates denitrification by determining release of nitrous oxide (N2O) from acetylene-treated soil.

acetylene-reduction assay- Estimates nitrogenase activity by measuring the rate of acetylene reduced to ethylene.

N-Acetylglucosamine and N-Acetylmuramic acid- Sugar derivatives in the peptidoglycan layer of bacterial cell walls.

acidophile- Organism that grows best under acid conditions (down to a pH of 1).

acid soil- Soil with a pH value < 6.6.

actinomycete- Nontaxonomic term applied to a group of high G + C base composition, Gram-positive bacteria that have a superficial resemblance to fungi. Includes many but not all organisms belonging to the order Actinomycetales.

activation energy- Amount of energy required to bring all molecules in one mole of a substance to their reactive state at a given temperature.

active site- Region of an enzyme where substrates bind.

adenosine triphosphate (ATP)- Common energy-donating molecule in biochemical reactions. Also an important compound in transfer of phosphate groups.

adsorption- Process by which atoms, molecules, or ions are taken up and retained on the surfaces of solids by chemical or physical binding.

aerobic- (i) Having molecular oxygen as a part of the environment. (ii) Growing only in the presence of molecular oxygen, as in aerobic organisms. (iii) Occurring only in the presence of molecular oxygen, as in certain chemical or biochemical processes such as aerobic respiration.

aerotolerant anaerobes- Microbes that grow under both aerobic and anaerobic conditions, but do not shift from one mode of metabolism to another as conditions change. They obtain energy exclusively by fermentation.

agar- Complex polysaccharide derived from certain marine algae that is a gelling agent for solid or semisolid microbiological media. Agar consists of about 70% agarose and 30% agaropectin. Agar can be melted at temperature above 100

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F

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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

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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

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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

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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

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obligate- (i) Adjective referring to an environmental factor (for example, oxygen) that is always required for growth. (ii) Organism that can grow and reproduce only by obtaining carbon and other nutrients from a living host, such as obligate symbiont.

oligonucleotide- Short nucleic acid chain, either obtained from an organism or synthesized chemically.

oligotroph- Microorganism specifically adapted to grow under low nutrient supply. Thought to subsist on the more resistant soil organic matter and be little affected by the addition of fresh organic materials. Sometimes a synonym for autochthonous.

oogonium- Specialized sexual structure formed as a female gametangium by funguslike organisms in the phylum Oomycota.

oospore- Thick-walled spore formed within an oogonium by fungus-like organisms in the phylum Oomycota.

operon- Cluster of genes whose expression is controlled by a single operator; typical in prokaryotic cells.

organelle- Membrane-enclosed body specialized for carrying out certain functions; found only in eukaryotic cells.

organic soil- Soil that contains a high percentage (>200 g kg-1, or >120-180 g kg-1 if saturated with water) of organic carbon.

organotroph- Organism that obtains reducing equivalents (stored electrons) from organic substrates.

osmosis- Diffusion of water through a membrane from a region of low solute concentration to one of higher concentration.

osmotic potential- Portion of total soil water potential due to the presence of solutes in soil water.

oven-dry soil-Soil that has been dried at 105