Microbiology Glossary

16S rrna Large polynucleotide (about 1,500 bases) that functions as a part of the small subunit of the ribosome of prokaryotes and from whose sequence evolutionary information can be obtained; the eukaryotic counterpart is 18s rrna.

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.

Acid soil Soil with a ph value < 6.6.

Acidophile Organism that grows best under acid conditions (down to a ph of 1).

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.

Activator Protein A regulatory protein that binds to specific sires in DNA and stimulates transcription; involved in positive control.

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.

Adhesion/attachment is a stable interaction of a cell with respect to a surface. Living cells actively excrete holdfast chemicals from their surface to anchor themselves to a substratum. This is referred to as adhesion or attachment.

ADP Adenosine di phosphate

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.

Aerobic Respiration Use of electron acceptors other then O2 in an electron transport based oxidation. Most common anaerobic electron acceptors are nitrate, sulfate, and carbonate.

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 A gelatinous substance derived from certain red algae; used as a solidifying agent in the preparation if nutrient media for growing microorganisms

Agarose Nonsulfated linear polymer consisting of alternating residues of D galactose and 3,6 anhydro L galactose. Agarose is extracted from seaweed, and agarose gels are often used as the resolving medium in electrophoresis.

Aggregate See soil aggregate

Akinete Thick walled resting cell of cyanobacteria and algae.

Alga (plural, algae) Phototrophic eukaryotic microorganism. Algae could be unicellular or multicellular. Blue green algae are not true algae; they belong to a group of bacteria called cyanobacteria.

Aliphatic Organic compound in which the main carbon structure is a straight chain.

Alkaline soil Soil having a ph value >7.3.

Alkalophile Organism that grows best under alkaline conditions (up to a ph of 10.5).

Alkane Straight chain or branched organic structure that lacks double bonds.

Alkene Straight chain or branched organic structure that contains at least one double bond.

Allochthonous flora Organisms that are not indigenous to the soil but that enter soil by precipitation, diseased tissues, manure, and sewage. They may persist for some time but do not contribute in a significant way to ecologically significant transformations or interactions.

Allosteric site Site on the enzyme other than the active site to which a nonsubstate compound binds. This may result in a conformational change at the active site so that the normal substrate cannot bind to it.

Amensalism (antagonism) Production of a substance by one organism that is inhibitory to one or more other organisms. The terms antibiosis and allelopathy also describe cases of chemical inhibition.

Amino group An NH2 group attached to a carbon skeleton as in the amines and amino acids.

Ammonification Liberation of ammonium (ammonia) from organic nitrogenous compounds by the action of microorganisms.

Amoeba (plural, amoebae) Protozoa that can alter their cell shape, usually by the extrusion of one or more pseudopodia.

AMP Adenosine mono phosphate

An /Aerobe An organism that grows in the presence of O2; may be facultative or obligate. / an organism that grows in the absence of O2. Some may even be killed by O2.

Anabolism (biosynthesis) Is the process by which a cell is built up from the simple nutrients obtained from the environment, and it results in the biochemical synthesis of new material. Biosynthesis is an energy requiring process, there are two kinds of energy sources light and chemicals.

Anaerobic (i) Absence of molecular oxygen. (ii) Growing in the absence of molecular oxygen, such as anaerobic bacteria. (iii) Occurring in the absence of molecular oxygen, as a biochemical process.

Anaerobic respiration Metabolic process whereby electrons are transferred from an organic, or in some cases, inorganic compounds to an inorganic acceptor molecule other than oxygen. The most common acceptors are nitrate, sulfate, and carbonate.

Anamorph Asexual stage of fungal reproduction in which cells are formed by the process of mitosis.

Anion exchange capacity Sum total of exchangeable anions that a soil can adsorb. Expressed as centimoles of negative charge per kilogram of soil.

Anoxic Literally "without oxygen." An adjective describing a microbial habitat devoid of oxygen.

Anoxygenic photosynthesis Type of photosynthesis in green and purple bacteria in which oxygen is not produced.

Antagonist Biological agent that reduces the number or disease producing activities of a pathogen.

Antheridium Male gametangium found in the phylum Oomycota (Kingdom Stramenopila) and phylum Ascomycota (Kingdom Fungi).

Anthropogenic Derived from human activities.

Antibiosis Inhibition or lysis of an organism mediated by metabolic products of the antagonist; these products include lytic agents, enzymes, volatile compounds, and other toxic substances.

Antibiotic Organic substance produced by one species of organism that in low concentrations will kill or inhibit growth of certain other organisms.

Antibody Protein that is produced by animals in response to the presence of an antigen and that can combine specifically with that antigen.

Antigen Substance that can incite the production of a specific antibody and that can combine with that antibody.

Antimicrobial agent an agent that kills or inhibits microbial growth.

Antiseptic Agent that kills or inhibits microbial growth but is not harmful to human tissue.

Apothecium Open ascoma of fungi in the phylum Ascomycota.

Arbuscular mycorrhiza (AM) Mycorrhizal type that forms highly branched arbuscules within root cortical cells.

Arbuscule Special "tree shaped" structure formed within root cortical cells by arbuscular mycorrhizal fungi.

Archaea Evolutionarily distinct group (domain) of prokaryotes consisting of the methanogens, most extreme halophiles and hyperthermophiles, and Thermoplasma.

Archaebacteria Older term for the Archaea.

Aromatic Organic compounds which contain a benzene ring, or a ring with similar chemical characteristics.

Arthropod Invertebrate with jointed body and limbs (includes insects, arachnids, and crustaceans).

Ascoma (plural, ascomata) Fungal fruiting body that contains ascospores; also termed an ascocarp.

Ascospore Spores resulting from karyogamy and meiosis that are formed within an ascus. Sexual spore of the Ascomycota.

Ascus (plural, asci) Saclike cell of the sexual state formed by fungi in the phylum Ascomycota containing ascospores.

Aseptic technique Manipulating sterile instruments or culture media in such a way as to maintain sterility.

Assimilable organic carbon (aoc) the fraction of total organic carbon in water that can be used for microbiological growth. It is measured by a growth potential assay.

Assimilatory nitrate reduction Conversion of nitrate to reduced forms of nitrogen, generally ammonium, for the synthesis of amino acids and proteins.

Associative dinitrogen fixation Close interaction between a free living diazotrophic organism and a higher plant that results in an enhanced rate of dinitrogen fixation.

Associative symbiosis Close but relatively casual interaction between two dissimilar organisms or biological systems. The association may be mutually beneficial but is not required for accomplishment of a particular function.

ATP The principle energy carrier of the cell, Adenosine tri phosphate

Autochthonous flora see oligotrophs.

Autolysis Spontaneous lysis.

Autoradiography Detecting radioactivity in a sample, such as a cell or gel, by placing it in contact with a photographic film.

Autotroph Organism which uses carbon dioxide as the sole carbon source.

Autotrophic nitrification Oxidation of ammonium to nitrate through the combined action of two chemoautotrophic organisms, one forming nitrite from ammonium and the other oxidizing nitrite to nitrate.

Auxotroph A mutant that has a growth factor requirement. Contrast with a prototroph.

Axenic Literally "without strangers." A system in which all biological populations are defined, such as a pure culture.

Bacillus Bacterium with an elongated, rod shape.

Bacteria All prokaryotes that are not members of the domain Archaea.

Bacteriochlorophyll Light absorbing pigment found in green sulfur and purple sulfur bacteria.

Bacteriocin Agent produced by certain bacteria that inhibits or kills closely related isolates and species.

Bacteriophage Virus that infects bacteria, often with destruction or lysis of the host cell.

Bacteroid Altered form of cells of certain bacteria. Refers particularly to the swollen, irregular vacuolated cells of rhizobia in nodules of legumes.

Base composition Proportion of the total bases consisting of guanine plus cytosine or thymine plus adenine base pairs. Usually expressed as a guanine + cytosine (G + C) value, e.g. 60% G+C.

Basidioma (plural, basidiomata) Fruiting body that produces basidia; also termed a basidiocarp.

Basidiospore Spore resulting from karyogamy and meiosis that are formed on a basidium that usually is formed on a basidium. Sexual spore of the Basidiomycota.

Basidium (plural, basidia) Clublike cell of the sexual state formed by fungi in the phylum Basidiomycota.

Binary fission Division of one cell into two cells by the formation of a septum. It is the most common form of cell division in bacteria.

Binomial nomenclature System of having two names, genus and specific epithet, for each organism.

Bioaccumulation Accumulation of a chemical substance in living tissue.

Bioavailability the availability of a nutrient for microbially mediated degradation or transformation. Typically, for a nutrient to be bioavailable, it must (1) be within physical proximity to the cell and (2) be dissolved in the aqueous phase, to be transported across the cell membrane. Thus, nutrients that are adsorbed to surfaces or sequestered into micropores that physically exclude cells are generally considered unavailable. Bioavailability should not be confused with recalcitrance, although distinguishing the two in the environment can be very difficult.

Biochemical oxygen demand (BOD) Amount of dissolved oxygen consumed in five days by biological processes breaking down organic matter.

Biocide / disinfectant an agent that is capable of killing microorganisms; however, it may not be 100% effective. In biofilm usage a chemical used to disinfect or remove biofilm in order to control a detrimental effect of the biofilm.

Biodegradable Substance capable of being decomposed by biological processes.

Bioelectric effect the undulating expansion and contraction of the charged biofilm matrix exopolymers created by the application of a dc field current which reverses polarity on a frequent basis. The net effect is to enhance the efficacy of antimicrobial agents against biofilm microorganisms.

Biofilm Microbial cells encased in an adhesive, usually a polysaccharide material, and attached to a surface.

Biogeochemistry Study of microbially mediated chemical transformations of geochemical interest, such as nitrogen or sulfur cycling.

Biomagnification Increase in the concentration of a chemical substance as it is progresses to higher trophic levels of a food chain.

Bioremediation Use of microorganisms to remove or detoxify toxic or unwanted chemicals from an environment.

Biosolid The resides of wastewater treatment. Formerly called sewage sludge.

Biosphere Zone incorporating all forms of life on earth. The biosphere extends from deep in sediment below the ocean to several thousand meters elevation in high mountains.

Biosynthesis Production of needed cellular constituents from other, usually simpler, molecules.

Biotechnology Use of living organisms to carry out defined physiochemical processes having industrial or other practical application.

Biotrophic Nutritional relationship between two organisms in which one or both must associate with the other to obtain nutrients and grow.

Blue green alga See cyanobacterium.

Brown rot fungus Fungus that attacks cellulose and hemicellulose in wood, leaving dark colored lignin and phenolic materials behind.

Budding Asexual reproduction (usually for yeast) beginning as a protuberance from the parent cell that grows and detaches to form a smaller, daughter cell.

Bug slang (derived from creepy crawlers in the field of entomology) used by microbiologists and others to refer casually to microorganisms such as bacteria, fungi, cyanobacteria, protozoa, microflagellates and other microscopic organisms.

Bulk density, soil Mass of dry soil per unit bulk volume (combined volume of soil solids and pore space).

Calvin cycle Biochemical route of carbon dioxide fixation in many autotrophic organisms.

Capsid Protein coat of a virus.

Capsule Compact layer of polysaccharide exterior to the cell wall in some bacteria.

Carbon cycle Sequence where carbon dioxide is converted to organic forms by photosynthesis or chemosynthesis, recycled through the biosphere, with partial incorporation into sediments, and ultimately returned to its original state through respiration or combustion.

Carbon fixation Conversion of carbon dioxide or other single carbon compounds to organic forms such as carbohydrates.

Carbon nitrogen (C/N) ratio Ratio of the mass of organic carbon to the mass of nitrogen in soil or organic material.

Carboxyl group A COOH group attached to a carbon skeleton as in the carboxylic acids and fatty acids.

Carcinogen Substance which causes the initiation of tumor formation. Frequently a mutagen.

Catabolism Biochemical processes involved in the breakdown of organic compounds, usually leading to the production of energy.

Catabolism The biochemical process involved in the breakdown of organic compounds, usually leading to the production of energy.

Catabolite repression Transcription level inhibition of a variety of inducible enzymes by glucose or other readily used carbon source.

Catalyst Substance that promotes a chemical reaction by lowering the activation energy without itself being changed in the end. Enzymes are a type of catalyst.

Cation exchange capacity (CEC) Sum of exchangeable cations that a soil can adsorb at a specific ph. Expressed as centimoles of positive charge per kilogram of soil (cmolc kg 1).

Cell cluster a discrete unit consisting of densely packed (1010 cells/ml cluster) bacterial cells (single or multi species) in a polymer matrix. Morphology of clusters can vary.

Cell Fundamental unit of living matter.

Cell membrane See cytoplasmic membrane.

Cell wall Layer or structure that lies outside the cytoplasmic membrane; it supports and protects the membrane and gives the cell shape.

Cell The fundamental unit of living matter. Embedded by a distinct membrane layers

Cellulose Glucose polysaccharide (with beta 1,4 linkage) that is the main component of plant cell walls. Most abundant polysaccharide on earth.

Chelate (chelator) Organic chemical that forms ring compound in which a metal is held between two or more atoms strongly enough to diminish the rate at which it becomes fixed by soil, thereby making it more available for plant and microbial uptake.

Chemiosmosis The use of ion gradients across membranes, especially protein gradients, to generate ATP, see proton motive force.

Chemoautotroph Organism that obtains energy from the oxidation of chemical, generally inorganic, compounds and carbon from carbon dioxide.

Chemoheterotroph Organism that obtains energy and carbon from the oxidation of organic compounds.

Chemolithotroph Organism that obtains energy from the oxidation of inorganic compounds and uses inorganic compounds as electron donors.

Chemo litothroph Organism obtaining its energy from the oxidation of inorganic compounds.

Chemoorganotroph Organism that obtains energy and electrons (reducing power) from the oxidation of organic compounds.

Chemo organotroph Organism obtaining its energy from the oxidation of organic compounds.

Chemostat Continuous culture device usually controlled by the concentration of limiting nutrient and dilution rate.

Chemotaxis Oriented movement of a motile organism with reference to a chemical agent. May be positive (toward) or negative (away) with respect to the chemical gradient.

Chlamydospore Thick walled resting structure that forms from the cell wall of a fungal hypha; usually formed under conditions where the hypha is no longer able to function optimally.

Chlorophyll Green pigment required for photosynthesis.

Chloroplast Chlorophyll containing organelle of photosynthetic eukaryotes.

Chromatography Any technique used to separate different species of molecules (or ions) by subjecting them to two different carrier phases mobile and stationary phases.

Chromosome Genetic element carrying information essential to cellular metabolism. Prokaryotes have a single chromosome, consisting of a circular DNA molecule. Eukaryotes contain more than one chromosome, each containing a linear DNA molecule complexed with specific proteins.

Chromosome A genetic element carrying genes essential to cellular metabolism. Prokaryota typically have a single chromosome, consisting of circular DNA molecule. Eukaryotic cells contain several chromosomes, each containing a linear DNA molecule complexed with specific proteins.

Chytrid Fungal organism in the phylum Chytridiomycota that consists of a spherical cell from which short thin filamentous branches (rhizoids) grow that resemble fine roots.

Ciliate Protozoan that moves by means of cilia on the surface of the cell.

Cilium (plural, cilia) Short, threadlike appendages that extend from the surface of some protozoa and beat rhythmically to propel them.

Citric acid cycle See tricarboxylic acid cycle.

Clamp connection Small branch of a fungal hypha that connects two compartments separated by a septum and helps to maintain a dikaryon in each hyphal compartment; characteristic of fungi in the phylum Basidiomycota.

Classification (i) Arrangement of organisms into groups based on mutual similarity or evolutionary relatedness. (ii) Systematic arrangement of soils into groups or categories on the basis of their characteristics.

Clay Soil particle < 0.002 mm in diameter.

Cleistothecium Closed ascocarp of fungi in the phylum Ascomycota.

Climax Most advanced successional community of plants capable of development under, and in dynamic equilibrium with, the prevailing environment.

Clone (i) Population of cells all descended from a single cell. (ii) Number of copies of a DNA fragment to be replicated by a phage or plasmid.

Cloning vector DNA molecule that is able to bring about the replication of foreign DNA fragments.

Coccus Spherical bacterial cells.

Codon A sequence of three purine and/or pyrimidine bases in mrna that encodes as specific amino acid.

Coenocytic Fungal hypha without crosswalls (septa), so that the nuclei present in the cytoplasm are free floating and mobile.

Coenzyme Low molecular weight chemical which participates in an enzymatic reaction by accepting and donating electrons or functional groups.

Cohesion Force holding a solid or liquid together, owing to attraction between like molecules.

Coliform bacteria members of the genus enterobacteriaceae; described as gram negative, nonsporing facultative rods that ferment lactose with gas formation within 48 hr @ 35oc. Used as indicator organisms in water and some foods.

Coliform Gram negative, nonspore forming facultative rod that ferments lactose with gas formation with 48 hours at 35C. Often an indicator organism for fecal contamination of water supplies. Escherichia coli and Enterobacter are important members.

Colloid fraction Organic and inorganic matter with very small particle size and a correspondingly large surface area per unit of mass.

Colonization Establishment of a community of microorganisms at a specific site or ecosystem.

Colony Clone of bacterial cells on a solid medium that is visible to the naked eye.

Colony forming unit (cfu) the minimum number of separable cells on the surface of or in semi solid agar medium which gives rise to a visible colony of progeny on the order of tens of millions of cells in number. Cfus may consist of pairs, chains and clusters as well as single cells.

Cometabolism Transformation of a substrate by a microorganism without deriving energy, carbon, or nutrients from the substrate. The organism can transform the substrate into intermediate degradation products but fails to multiply at its expense.

Commensalism Interaction between organisms where one organism benefits from the association while the second organism remains unaffected.

Community All organisms that occupy a common habitat and interact with one another.

Competent In a genetic sense, the ability to take up DNA.

Competition Rivalry between two or more species for a limiting factor in the environment that usually results in reduced growth of participating organisms.

Complementary In reference to base pairing, the ability of two polynucleotide sequences to form a double stranded helix by hydrogen bonding between bases in the two sequences.

Complex medium Medium whose precise chemical composition is unknown. Also called undefined medium.

Compost Organic residues which have been mixed, piled, and moistened, with or without addition of fertilizer and lime, and generally allowed to undergo thermophilic decomposition until the original organic materials are substantially altered or decomposed.

Concentration Gradient The concentration difference of a substance per unit distance; e.g. Across cellmembrane.

Conidiophore Aerial hypha bearing conidia.

Conidium (plural, conidia) Nonmotile, asexual spore resulting from mitotic nuclear division and formed from the ends or sides of a hypha; produced in abundant numbers by the asexual phase of soil fungi in the phyla Ascomycota and Basidiomycota.

Conjugation In prokaryotes, transfer of genetic information from a donor cell to a recipient cell by cell to cell contact.

Conjugative plasmid Self transmissible plasmid; a plasmid that encodes all the functions needed for its own intercellular transmission by conjugation.

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.

Constitutive enzyme Enzyme always synthesized by the cell regardless of environmental conditions.

Covalent Nonionic chemical bond formed by a sharing of electrons between two atoms.

Cristae Enfoldings of the inner mitochondrial membrane, which form a series of crests or ridges containing the electron transport chain involved in ATP formation.

Cross feeding (i) Specific type of syntrophy where two populations cooperate to metabolize a compound. (ii) One organism consuming products excreted by another organism.

Ctc a compound (5 cyano 2,3 ditolyl tetrazolium chloride) that is fluorogenic, producing intracellular crystals, in response to bacterial respiration.

Culture Population of microorganisms cultivated in an artificial growth medium. A pure culture is grown from a single cell; a mixed culture consists of two or more microbial species or strains growing together.

Cyanobacterium Prokaryotic, oxygenic phototrophic bacterium containing chlorophyll a and phycobilins, formerly the "blue green algae."

Cyclic photophosphorylation Formation of ATP when light energy is used to move electrons cyclically through an electron transport chain during photosynthesis.

Cyst Resting stage formed by some bacteria, nematodes, and protozoa in which the whole cell is surrounded by a protective layer; not the same as endospore.

Cytochrome Iron containing porphyrin ring (e.g., heme) complexed with proteins which act as electron carriers in an electron transport chain.

Cytoplasm Cellular contents inside the cell membrane, excluding the nucleus.

Cytoplasmic Membrane The permeability barrier of the cell, separating the cytoplasma from the environment.

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.

Detachment transfer of biofilm particulate constituents (cells, polymers, precipitates) from the biofilm to the fluid bathing the biofilm.

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 (deoxyribonucleic acid) A double chain of linked nucleotides (having deoxyribose as their sugars); the fundamental substance of which genes are composed;

DNA Double Helix Two interlocking helixes joined by hydrogen bonds between the pairs purinepyrimidine bases.

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.

DNA Replication Semiconservative replication, where one strand determines the sequence of the complimentary strand (DNA synthesis).

DNA Sequence The linear assembly of purine / pyrimidine nucleotides along a DNA strand.

DNA Topoisomerase Enzyme unwinding the tightly coiled DNA arrangement, for DNA replication.

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.

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.

Electron Acceptor A substance that accepts electrons during an oxidation reduction reaction. An electron acceptor is an oxidant.

Electron Donor A compound that donates electrons during 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 phosphorilation Synthesis of ATP involving a membrane associated electron transport chain and the creation of a proton motive force. Also called oxidative phosphorilation.

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.

Endoenzyme Enzyme that operates along the internal portions of a polymer.

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

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.

Endospore A differentiated cell formed within the cells of certain gram positive bacteria and extremely resistant to heat as well as to other harmful agents.

Energetic Reactions Chemical reactions requiring / liberating chemical energy.

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 A protein functioning as a catalyst in living organisms, which promotes specific reactions or groups of 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.

Eps generic term referring to polymers of varying chemical composition that are excreted outside the cell. Synonymous with exopolysaccharide, exocellular polymer, extracellular polymer, exopolymer. Term does not distinguish between bound polymer (capsule) and polymer excreted into the surrounding environment. In biofilms, eps may refer to the polymers that extend between cells, forming a matrix and anchoring the cells to each other and to the substratum.

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 R. A chemical reaction that proceeds with the liberation of energy, see endergonic reaction.

Exergonic reaction Chemical reaction that proceeds with the liberation of energy.

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

Exon The coding sequences in a split gene of eukaryota.

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.

Extracellular Outside the cell.

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

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

Facultative A qualifying adjective indicating that an organism is able to grow either in the presence or absence of an environmental factor (e.g., facultative aerobe).

FAD flavinadeninedineucleotide, a coenzyme formed by the condensation of riboflavin phosphate and adenylic acid; it performs an important function in electron transport (oxidation of fuel molecules) and is a prostethic group for some enzymes.

FADH intermediate to FADH2; only one site of the isoalloxazine ring is occuppied;

FADH2 isoalloxazine ring can occupy 2e and 2H+;

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.

Fermentation Catabolic reactions producing ATP in which organic compounds serve as both primary electron donor and ultimate electron acceptor.

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 immunoglobulin molecule (antibody) coupled with a fluorescent dye.

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.

Frameshift the genetic code is read three bases at a time, if reading begins at either the second or third base of a codon, a faulty product usually results. This is called a frameshift (the reading frame refers to the pattern of reading).

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.

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 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 Disruption Use of both in vitro and in vivo recombination to substitute an easily selected mutant gene for a wild type 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.

Gene A unit of hereditary; a segment of DNA specifying a particular portion or polypeptide chain, a trna or rrna.

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

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).

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

Genome The complete sets of genes present in an organism;

Genotype The precise genetic constitution of an organism; information encoded by the genome;

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

Gibb's free energy See free energy.

Glycocalyx extracellular polymeric material produced by some bacteria. Term initially applied to the polysaccharide matrix excreted by epithelial cells forming a coating on the surface of epithelial tissue. General term for polysaccharide compounds outside the bacterial cell wall. Also called slime layer, eps, or matrix polymer.

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.

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.

Gram Negative Cell wall containing relatively little peptidoglycan (10%) but contains an lipo polysaccharide (LPS) layer with embedded complex macromolecules

Gram Positive A procaryotic cell whose cell wall consists chiefly of peptidoglycan (90%) and lacks the outer membrane of Gram negative cells.

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

Grazing See predation.

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

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

Growth limiting factor is parameter which controls the replication rate of a bacterium or other cell in the environment where that cell resides (i.e., temperature, hydrogen ion concentration, ionic strength, etc.).

Growth limiting nutrient a compound or ion which, when added to the environment in which a population of cells resides, results in an increase in cell biomass. Also known as limiting substrate.

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

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

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

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 bacteria those bacteria that require an organic carbon source for growth; i.e. Derive energy and carbon from organic compounds.

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

Heterotrophic plate count bacteria (hpc) those bacteria that will grow on nonselective heterotrophic medium plates.

Holdfast polymers excreted by living organisms that mediate a stable interaction between the organism and a solid substratum. Examples of holdfast molecules excreted by microorganisms include pili, fimbriae, stalks, and exopolysaccharides.

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 An 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.

Hybridisation Formation of a double nucleic acid molecule with strands derived from different sources by complementary base pairs; see bacterial systematics.

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.

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

Hydrogen Bonds A weak chemical bond between a hydrogen atom and a second, more electronegative element, usually an oxygen or nitrogen atom.

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.

Hydrolysis Breakdown of a polymer into smaller units, usually momomers, by addition of water, digestion.

Hydrophobic Interactions Attractive forces between molecules due to the positioning of nonhydropholic portions of two molecules.

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

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.

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.

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.

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

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.

Immunoglobulin Antibody.

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.

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

Induction The process by which an enzyme is synthesized 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 m to 1 mm.

Inhibition Absorption of water and swelling of colloidal materials because of the absorption of water molecules onto the internal surface of the materials.

Injury reversible phenotypic response of bacteria exposed to sublethal stressors.

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.

Insertion A genetic phenomenon in which a piece of DNA is inserted into the middle of a gene.

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

Intracellular Inside the cell.

Introns The intervening non coding sequences in a split gene of eukaryota.

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.

Isozyme See isoenzyme.

Karyogamy Fusion in a cell of haploid (N) nuclei to form a diploid (2N).

Kilobase (kb) A 1000 base fragment of nucleic acid. A kilobase pair is a fragment containing 1000 base pairs.

Koch's Postulates Set of laws formulated by Robert Koch to prove that an organism is the causal agent of disease.

Krebs Cycle (citric acid cycle, or tricarboxylic acid cycle) A series of steps by which pyruvate is oxidized completely to CO2, also forming NADH, which allows ATP production.

K strategy Ecological strategy where organisms depend on physiological adaptations to environmental resources. K strategists are usually stable and permanent members of the community.

Lag phase Period after inoculation of fresh growth medium during which population numbers do not increase.

Lamella (plural, lamellae) (i) A thin layer, platelike arrangement or membrane. (ii) Layers of protoplasmic membranes within the chloroplast that contain the photosynthetic pigments.

Latin binomial See binomial nomenclature.

Leaching (i) Removal of valuable metals from ores by microbial action. (ii) The removal of materials in solution from the soil.

Lectins Plant proteins with a high affinity for specific sugar residues.

Leghemoglobin Iron containing, red pigment(s) produced in root nodules during the symbiotic association between rhizobia and leguminous plants. The pigment is similar but not identical to mammalian hemoglobin.

Lichen Fungus and an alga or a cyanobacterium living in symbiotic association.

Ligand Molecule, ion, or group bound to the central atom in a chelate or a coordination compound.

Lime, agricultural Soil amendment containing calcium carbonate, magnesium carbonate or other materials to neutralize soil acidity and furnish calcium or magnesium or both for plant growth.

Limiting substrate see growth limiting nutrient for basic definition. If all nutrients are in perfect proportion there is balanced growth. If all nutrients are balanced but not present in sufficient quantity, growth is substrate limited. If there is an excess of nutrient in the bulk fluid, but it is not reaching biofilm bacteria because of transport limitations, growth is transport limited.

Lipopolysaccharide (LPS) Complex lipid structure containing unusual sugars and fatty acids found in many Gram negative bacteria.

Lithotroph Organism that uses an inorganic substrate such as ammonia or hydrogen as an electron donor in energy metabolism. There are two types of lithotrophs chemolithotroph and photolithotroph.

Litter Surface layer of the forest floor consisting of freshly fallen leaves, needles, twigs, stems, bark, and fruits.

Lophotrichous Having a tuft of polar flagella.

Luminescence Production of light.

Luxury uptake The absorption by plants of nutrients in excess of their need for growth. Luxury contents accumulated during early growth may be used for later growth.

Lysis Rupture of a cell, resulting in loss of cell contents.

Lysis Rupture of a cell, resulting in loss of cell contents.

Lysogen A prokaryota containing a prophage, see also temperate virus.

Lysogeny An association where a prokaryote contains a prophage and the virus genome is replicated in synchrony with the host chromosome.

Lysosome Cell organelle containing digestive enzymes.

Macrofauna Soil animals that are > 1000 micrometers in length (e.g., vertebrates, earthworms, and large arthropods).

Macromolecule Large molecule formed from the connection of a number of small molecules.

Macronutrient A substance required in large amounts for growth, usually attaining a concentration of > 500 mg kg 1 in mature plants. Usually refers to N, P, K, Ca, Mg, and S.

Macropore Larger soil pores, generally having a minimum diameter between 30 and 100 micrometers, from which water drains readily by gravity.

Magnetosomes Small particles of Fe3O4 present in cells that exhibit magnetotaxis.

Manure Excreta of animals, with or without an admixture of bedding or litter, fresh or at various stages of decomposition or composting. In some countries the term may denote any fertilizer material.

Mass flow (nutrient) Movement of solutes associated with net movement of water.

Matric potential Portion of the total soil water potential due to the attractive forces between water and soil solids as represented through adsorption and capillarity.

Medium (plural, media) Any liquid or solid material prepared for the growth, maintenance, or storage of microorganisms.

Meiosis In eukaryotes, reduction division, the process by which the change from diploid to haploid occurs.

Membrane Thin layer composed of a phosopholipid bilayer, see also cytoplasmic membrane.

Mesofauna Soil animals between 200 to1000 micrometers in length, including nematodes, oligochaete worms, smaller insect larvae, and small arthropods.

Mesophile Organism whose optimum temperature for growth falls in an intermediate range of approximately 15 to 40C.

Messenger RNA (mrna) RNA molecule transcribed from DNA, which contains the information to direct the synthesis of a particular protein.

Metabolism (Gk. Metabole, change) All biochemical reactions in a cell, both anabolic and catabolic.

Methanogenesis Biological production of methane.

Methanogenic bacterium (methanogen) Methane producing prokaryote; member of the Archaea.

Methanotroph Organism capable of oxidizing methane.

Microaerophile Organism that requires a low concentration of oxygen for growth. Sometimes indicates an organism that will carry out its metabolic activities under aerobic conditions but will grow much better under anaerobic conditions.

Microaggregate Clustering of clay packets stabilized by organic matter and precipitated inorganic materials.

Microbial biomass Total mass of microorganism alive in a given volume or mass of soil.

Microbial population Total number of living microorganisms in a given volume or mass of soil.

Microbiology Study of microorganisms.

Microcosm A community or other unit that is representative of a larger unity.

Microenvironment Immediate physical and chemical surroundings of a microorganism.

Microfauna Protozoa, nematodes and arthropods generally < 200 micrometers long.

Microflora Bacteria (including actinomycetes), fungi, algae, and viruses.

Microhabitat Clusters of microaggregates with associated water within which microbes function. May be composed of several microsites (e.g., aerobic and anaerobic).

Micrometer One millionth of a meter, or 10 6 meter, the unit usually used for measuring microorganisms.

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.

Microorganism (microbe) Living organism too small to be seen with the naked eye (< 0.1 mm); includes bacteria, fungi, protozoans, microscopic algae, and viruses.

Micropore Relatively small soil pore, generally found within structural aggregates and having a diameter < 30 micrometers.

Microsite Small volume of soil where biological or chemical processes differ from those of the soil as a whole, such as an anaerobic microsite of a soil aggregate or the surface of decaying organic residues.

Mineralization Conversion of an element from an organic form to an inorganic state as a result of microbial decomposition.

Minor elements See micronutrients.

Mitochondrion (plural, mitochondria) Eukaryotic organelle responsible for processes of respiration and oxidative phosphorylation.

Mitochondrium Eukaryotic organelle responsible for processes of respiration and electron transport phosphorylation (ATP generation).

Mitosis Highly ordered process by which the nucleus divides in eukaryotes.

Mixotroph Organism able to assimilate organic compounds as carbon sources while using inorganic compounds as electron donors. Compare with autotroph and heterotroph.

Moisture content See water content.

Moisture characteristic curve See water retention curve.

Moisture release curve See water retention curve.

Mold A filamentous fungus.

Molecule Result of two or more atoms combining by chemical bonding.

Monoclonal antibody Antibody produced from a single clone of cells. This antibody has uniform structure and specificity.

Monokaryon Fungal hypha in which compartments contain one nucleus.

Monomer A building block of a monomer.

Most probable number (MPN) Method for estimating microbial numbers in soil based on extinction dilutions.

Motility Movement of a cell under its own power.

Mucigel Gelatinous material at the surface of roots grown in normal nonsterile soil. It includes natural and modified plant mucilages, bacterial cells, and their metabolic products (e.g., capsules and slimes), and colloidal mineral and organic matter from the soil.

Mucilage Gelatinous secretions and exudates produced by plant roots and many microorganisms..

Mulch (i) Any material such as straw, sawdust, leaves, plastic film, and loose soil, that is spread upon the surface of the soil to protect the soil and plant roots from the effects of raindrops, soil crusting, freezing, or evaporation. (ii) To apply mulch to the soil surface.

Municipal solid waste Combined consumer and commercial waste generated within a defined geographic area

Murein see peptidoglycan.

Mushroom Large, sometimes edible, fruiting body produced by some fungi.

Mutagen An agent that induces mutation, such as radiation or certain chemicals.

Mutant A strain differing from its parent because of mutation.

Mutation An inheritable change in the base sequence of the DNA of an organism.

Mutualism Interaction between organisms where both organisms benefit from the association.

Mycelium (plural, mycelia) Mass of hyphae that form the vegetative body of many fungal organisms.

Mycophage see mycovirus.

Mycophagous Organisms that consume fungi, such as mycophagous nematodes.

Mycoplasma Group of bacteria without a cell walls that do not revert to walled forms. Phylogenetically related to clostridia.

Mycorrhiza Literally "fungus root." The symbiotic association between specific fungi with the fine roots of higher plants.

Mycorrhizosphere Unique microbial community that forms around a mycorrhiza.

Mycovirus Virus that infects fungi.

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

NAD nicotinamidadeninedinucleotide, a widely distributed coenzyme in living organisms; made up of adenine, nicotinamide, and 2 molecules each of d ribose and phosphoric acid; it serves as an electron acceptor in many oxidation reactions of cell respiration see biochemistry DNA RNA.

NAD+ oxidized form; is a major electron acceptor in the oxidation of fuel molecules (respiratory chain); with the reactive part the pyridine ring on top;

NADH reduced form of NAD+; in the oxidation process accepts a H ion and two electrons, which are equivalent to a hydride ion;

NADP+ oxidized form, a coenzyme that functions as an electron acceptor in many of the reduction reactions of biosynthesis; similar in structure to NAD+ except that it contains an extra phosphate; It is exclusively used as an e donor in reductive biosynthesis, whereas NADH is oxidized by the respiratory chain to generate ATP.

Nanopore Soil pore having dimensions measured in nanometers. Materials encased in nanopores are beyond the reach of microorganisms and enzymes.

Necrosis Damage of living tissues because of infection or injury.

Necrotrophic Nutritional mechanism by which an organism produces a battery of hydrolytic enzymes to kill and break down host cells and then absorb nutritional compounds from the dead organic matter.

Nematode Multicellular eukaryote defined as an unsegmented, usually microscopic roundworm. Various species feed on plants, animals, fungi, and bacteria.

Neutralism Lack of interaction between two organisms in the same habitat.

Niche Functional role of a given organism within its habitat.

Nicotinamide adenine dinucleotide (NAD+) Important coenzyme, functioning as a hydrogen and electron carrier in a wide range of redox reactions; the oxidized form of the coenzyme is written NAD+, the reduced form as NADH.

Nicotinamide adenine dinucleotide phosphate (NADP+) Important coenzyme, functioning as a hydrogen and electron carrier in a wide range of redox reactions; the oxidized form of the coenzyme is written NADP+, the reduced form as NADPH.

Nitrate reduction (biological) Process whereby nitrate is reduced by plants and microorganisms to ammonium for cell synthesis (nitrate assimilation, assimilatory nitrate reduction) or to various lower oxidation states (N2, N2O, NO,) by bacteria using nitrate as the terminal electron acceptor in anaerobic respiration.

Nitrification Biological oxidation of ammonium to nitrite and nitrate, or a biologically induced increase in the oxidation state of nitrogen.

Nitrifying bacteria Chemolithotrophs capable of carrying out the transformations from NH3 to NO2 or NO2 to NO3 .

Nitrogen cycle Sequence of biochemical changes wherein nitrogen is used by a living organism, transformed upon the death and decomposition of the organism, and converted ultimately to its original state of oxidation.

Nitrogen fixation See dinitrogen fixation.

Nitrogenase Specific enzyme system required for biological N2 fixation.

Nodule bacteria see rhizobia.

Nodule See root nodule.

Nodulins Unique proteins produced in root hairs or nodules in response to rhizobial infection.

Nomenclature System of naming organisms.

Nonpolar Possessing hydrophobic (water repelling) characteristics and not easily dissolved in water.

Northern blot Hybridization of single stranded nucleic acid (DNA or RNA) to RNA fragments immobilized on a filter.

Nucleic Acid A polymer of nucleotides. (see genetics, biochemistry DNA, RNA).

Nucleoid Aggregated mass of DNA that makes up the chromosome of prokaryotic cells.

Nucleophilic compound Chemical that attracks or is drawn to electron deficient regions in other chemicals; reducing agents act as nucleophilic compounds.

Nucleoside Nucleotide without the phosphate group.

Nucleotide A single unit of nucleic acid, composed of a phosphate, a 5 C sugar (either ribose or deoxyriboose), and a purine or a pyrimidine.

Nucleus Membrane enclosed structure containing the genetic material (DNA) organized in chromosomes.

Nutrient A substance taken by a cell from its environment and used in catabolic or anabolic reactions.

Obligate A qualifying adjective referring to an environmental f actor always required for growth (e.g., obligate anaerobe).

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 s membrane from s 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 105C until it reaches constant mass.

Oxic Containing oxygen; aerobic. Usually used in reference to a microbial habitat.

Oxidation Process by which a compound gives up electrons, acting as an electron donor, and becomes oxidized.

Oxidation state Number of electrons to be added (or subtracted) from an atom in a combined state to convert it to the elemental form.

Oxidation A process by which a compound gives up electrons, acting as an electron donor, and becomes oxidized (mostly by oxygen, leading to this terminus.

Oxidation Reduction (redox) reaction A coupled pair of reactions, in which one compound becomes oxidized, while another becomes reduced and takes up the electrons released in the oxidation reaction.

Oxidative Phosphorylation (electron transport) The non phototrophic production of ATP at the expense of a proton motive force formed by electron transport.

Oxygenic photosynthesis Use of light energy to synthesize ATP and NADPH by noncyclic photophosphorylation with the production of oxygen from water.

Parasexual cycle Nuclear cycle in which genes of haploid nuclei recombine without meiosis.

Parasitism Feeding by one organism on the cells of a second organism, which is usually larger than the first. The parasite is, to some extent, dependent on the host at whose expense it is maintained.

Particle density Density of the soil particles, the dry mass of the particles being divided by the solid (not bulk) volume of the particles, in contrast with bulk density.

Particle size Effective diameter of a particle measured by sedimentation, sieving or micrometric methods.

Pasteurization Process using mild heat to reduce microbial numbers in heat sensitive materials.

Pathogen an organism capable of producing disease in a host.

Pathogen Organism able to inflict damage on a host it infects.

Pathogenicity Ability of a parasite to inflict damage on the host.

Pathogen suppressive soil Soil where a pathogen does not establish or persist, a pathogen establishes but causes little or no damage, or a pathogen causes disease for a while, but the disease becomes less important even though the pathogen persists in soil.

Peat Unconsolidated soil material consisting largely of undecomposed, or only slightly decomposed, organic matter accumulated under conditions of excessive moisture.

Pectin Important component of the plant cell walls containing chains of galacturonic acid that is often esterified with a methyl group.

Pellicle Relatively rigid layer of proteinaceous elements just beneath the cell membrane in many protozoa and algae.

Peptide Bonds A type of covalent bond joining amino acids in a polypeptide.

Peptidoglycan The rigid layer of cell walls of Bacteria, a thin sheet composed of N acetylglucosamine, N acetylmuramic acid, and a few amino acids; also called murein.

Peribacteroid membrane Plant derived membrane surrounding one to several rhizobia within host cells of legume nodules

Periplasmic space Area between the cell membrane and the cell wall in Gram negative bacteria, containing certain enzymes involved in nutrition.

Perithecium Flask shaped ascocarp open at the tip; containing asci of fungi in the phylum Ascomycota.

Peritrichous flagellation Having flagella attached to many places on the cell surface.

Permanent wilting point Greatest water content of a soil at which indicator plants, growing in that soil wilt and fail to recover when placed in a humid chamber. Often estimated by the water content at 1.5 mpa soil matric potential.

Ph Negative logarithm of the hydrogen ion activity. The degree of acidity (or alkalinity) of a soil as determined by means of a glass or other suitable electrode or indicator at a specified moisture content or soil water ratio, and expressed in terms of the ph scale.

Phage See bacteriophage.

Phagotrophic Form of feeding where animals, such as protozoans, engulf particulate nutrients, such as bacterial cells or detritus.

Phenotype Observable properties of an organism.

Phenotype The observable properties of an organism; i.e. Information expressed by the genome;

Phosphobacterium Bacterium that is especially good at solubilizing the insoluble inorganic phosphate in soil.

Phosphodiester B. A type of covalent bond linking nucleotides together in a polynucleotide.

Phosphodiester bond Type of covalent bond linking nucleotides together in a polynucleotide.

Phospholipid Lipids containing a substituted phosphate group and two fatty acid chains on a glycerol backbone.

Phosphorus cycle sequence of transformations undergone by phosphorus where it is transformed between soluble and insoluble, and organic and inorganic forms.

Phosphorylation Synthesis of high energy phosphate bonds as ATP.

Photic zone Uppermost layer of a body of water or soil that receives enough sunlight to permit the occurrence of photosynthesis.

Photoautotroph Organism able to use light as its sole source of energy and carbon dioxide as sole carbon source.

Photoheterotroph Organism able to use light as a source of energy and organic materials as carbon source.

Photophosphorylation Synthesis of high energy phosphate bonds, as ATP, using light energy.

Photosynthesis Process of using light energy to synthesize carbohydrates from carbon dioxide.

Phototaxis Movement toward light.

Phototroph Organism that uses light as the energy source to drive the electron flow from the electron donors, such as water, hydrogen, or sulfide.

Phycobilin Water soluble pigment that occurs in cyanobacteria and functions as the light harvesting pigments for Photosystem II.

Phylogeny Ordering of species into higher taxa and the construction of evolutionary trees based on evolutionary (genetic) relationships.

Pilus (plural pili) Fimbria like structure that is present on fertile cells and is involved in DNA transfer during conjugation. Sometimes called sex pilus.

Plant growth promoting rhizobacteria (PGPR) Broad group of soil bacteria that exert beneficial effects on plant growth usually as root colonizers. Many members of the genus Pseudomonas.

Plaque A zone of lysis or cell inhibition caused by virus infection of a lawn of sensitive cells.

Plasma membrane See cytoplasmic membrane.

Plasmid an extrachromosomal genetic element found in bacteria, not essential for growth. Usually contains genetic information for resistance to an antimicrobial agent or for degradation of additional substrates.

Plasmogamy Fusion of the contents of two cells, including cytoplasm and nuclei.

Plastid Specialized cell organelles containing pigments or protein materials.

Plate count Number of colonies formed on a solid culture medium when uniformly inoculated with a known amount of soil, generally as a dilute soil suspension. The technique estimates the number of certain organisms present in the soil sample.

Polar flagellation Condition of having flagella attached at one end or both ends of the cell.

Polar Possessing hydrophilic characteristics and generally water soluble.

Poly beta hydroxybutyrate (PHB) Common storage material of prokaryotic cells consisting of beta hydroxybutyrate or other beta alkanoic acids.

Polyclonal antiserum Mixture of antibodies to a variety of antigens or to a variety of determinants on a single antigen.

Polymer A large molecule formed by polymerisation of monomeric units.

Polymerase chain reaction (PCR) Method for amplifying DNA in vitro, involving the use of oligonucleotide primers complementary to nucleotide sequences in target genes and the copying of the target sequences by the action of DNA polymerase.

Polymerase Chain Reaction (PCR) A method used to amplify a specific DNA sequence in vitro by repeated cycles of synthesis using specific primers and DNA polymerase.

Polypetide Bonds Several amino acids linked together by peptide bonds.

Polysaccharide Long chain of monosaccharides (sugars) linked by glycosidic bonds.

Polysome Strings of ribosomes attached by strands of mrna.

Pore space Portion of soil bulk volume occupied by soil pores.

Porin A protein channel in the lipopolysaccharide layer of Gram negative bacteria.

Porosity Volume of pores in a soil sample (nonsolid volume) divided by the bulk volume of the sample.

Pour plate Method for performing a plate count of microorganisms. A known amount of a serial dilution is placed in a sterile Petri dish and then a melted agar medium is added and the inoculum mixed well by gently swirling. After growth the number of colony forming units is counted.

Predation Relationship between two organisms whereby one organism (predator) engulfs or captures and digests the second organism (prey).

Pribnow Box The consensus sequence TATAAT located approximately 10 base pairs upstream from the transcription start site for polymerase.

Primary producer Organism that adds biomass to the ecosystem by synthesizing organic molecules from carbon dioxide and simple inorganic nutrients.

Primary Structure In an informational macromolecule, such as a polypeptide or nucleic acid, the precise sequence of monomeric units.

Primer Molecule (usually a polynucleotide) to which DNA polymerase can attach the first nucleotide during DNA replication.

Primer A molecule (usually a polynucleotide) to which DNA polymerase can attach the first nucleotide during DNA replication.

Prion An infectious agent whose extracellular form may contain no nucleic acid.

Prokaryota A cell or organism lacking a unit membrane bound (true) nucleus and other organelles, usually having its DNA in a single circular molecule.

Prokaryote Organism lacking a unit membrane bound nucleus and other organelles, usually having its DNA in a single circular molecule.

Promoter Site on DNA where the RNA polymerase binds and begins transcription.

Promoter The site on DNA where the RNA polymerase binds and begins transcription.

Propagule Cell unit capable of developing into a complete organism.

Prophage State of the genome of a temperate virus when it is replicating in synchrony with that of the host, typically integrated into the host genome.

Prosthetic group Tightly bound, nonprotein portion of an enzyme; not the same as coenzyme.

Protein (Gk. Proteios, primary) A complex organic compound composed of many (about 100) aminoacids joined together by peptide bonds. (see polypeptide chain).

Protista Old taxonomic term referring to algae, fungi, and protozoa (collectively, the eukaryotic protists), and the prokaryotes.

Protocooperation See synergism.

Proton motive force (PMF) Energized state of a membrane created by expulsion of protons through action of an electron transport chain.

Proton Motive Force An energized state of a membrane created by expulsion of protons through action of an electron transport chain.

Protoplasm Complete cellular contents, cytoplasmic membrane, cytoplasm, and nucleus; usually considered the living portion of the cell, thus excluding those layers peripheral to the cell membrane.

Protoplasma The complete cellular contents, cytoplasmic membrane, cytoplasma, and nucleus; considered to be the living portion of the cell, thus excluding those layers peripheral to the cytopolasmic membrane.

Protoplast Cell from which the wall has been removed.

Protozoan (plural, protozoa) Unicellular eukaryotic microorganisms that move by either protoplasmic flow (amoebae), flagella (flagellates) or, cilia (ciliates). Most species feed on bacteria, fungi, or detrital particles

Pro V. (prophage) The state of the genome of a temperate virus when it is replicated in synchrony with that of the host, typically integrated into the host genome.

Provirus See prophage.

Pseudomonad Member of the genus Pseudomonas, a large group of Gram negative, obligately respiratory (never fermentative) bacteria.

Pseudopodium (plural, pseudopodia) Protrusion of an amoeboid cell formed by the extrusion or streaming of the cytoplasm (but still enclosed in the membrane) for the purpose of movement or feeding.

Psychrophile Organism able to grow at low temperatures and showing a growth temperature optimum < 15C.

Pure culture Population of microorganisms composed of a single strain. Such cultures are obtained through selective laboratory procedures and are rarely found in a natural environment.

Q10 Relative increase in a reaction rate with temperature. It is expressed as the increase over a 10C interval.

Quartiary Structure of Protein The number and arrangement of individual polypeptides in the final protein molecule.

Quinone Found in the bacterial plasma membrane are of essential need for the electron transport chain and oxidative phosphorylation (ATP generation as a result of the transfer of electrons from NADH or FADH2 to O2 by a series of electron carriers).

Reannealing Process where two complementary single strands of DNA automatically hybridize back into a single, double stranded molecule upon cooling.

Recalcitrance the inability of a nutrient to be degraded or transformed by a cell. Possible reasons for recalcitrance include the lack of necessary membrane transport mechanisms for the chemical or lack of enzymes that facilitate its transformation or degradation. Recalcitrance should not be confused with bioavailability, although distinguishing the two in the environment can be very difficult.

Recalcitrant Resistant to microbial attack.

Recombinant DNA DNA molecule containing DNA originating from two or more sources.

Recombination Process by which genetic elements in two separate genomes are brought together in one unit.

Redox See oxidation reduction reaction.

Reducing equivalent (power) Electrons stored in reduced electron carriers such as NADH, NADPH and FADH2.

Reduction potential Inherent tendency of a compound to act as an electron donor or an electron acceptor. Measured in millivolts.

Reduction A process by which a compound accepts electrons to become reduced.

Reductive dechlorination Removal of Cl as Cl from an organic compound by reducing the carbon atom from C Cl to C H.

Remediation See bioremediation.

Replication Conversion of one double stranded DNA molecule into two identical double stranded DNA molecules.

Repression Process by which the synthesis of an enzyme is inhibited by the presence of an external substance (the repressor).

Repressor Protein A regulatory protein which binds to specific sites on DNA and blocks transcription; involved in negative control.

Respiration Catabolic reactions producing ATP in which either organic or inorganic compounds are primary electron donors and organic or inorganic compounds are ultimate electron acceptors. An intercellular process in which molecules, particularly pyruvate in the Krebs Cycle, are oxidized with the release of energy. The complete breakdown of sugar or other organic compounds to CO2 and H2O is termed aerobic respiration, although the first step in this process are anaerobic.

Restriction endonuclease (restriction enzyme) Enzyme that recognizes and cleaves specific DNA sequence, generating either blunt or single stranded (sticky) ends.

Restriction fragment length polymorphism (RFLP) Method to identify differences between similar genes from different organisms. Digestion of genes with restriction endonucleases followed by separation of the resulting fragments by gel electrophoresis yields banding patterns that are characteristic of the individual gene.

Retrovirus Virus containing single stranded RNA as its genetic material and producing a complementary DNA by action of the enzyme reverse transcriptase.

Reverse transcription Process of copying information found in RNA into DNA.

Rhizobacteria Bacteria that aggressively colonize roots.

Rhizobia Bacteria capable of living symbiotically in roots of leguminous plants, from which they receive energy and often fix molecular dinitrogen. Collective common name for Rhizobium and closely related genera.

Rhizoid Rootlike structure that helps to hold an organism to a substrate.

Rhizomorph Mass of fungal hyphae organized into long, thick strands usually with a darkly pigmented outer rind and containing specialized tissues for absorption and water transport.

Rhizoplane Plant root surfaces and usually strongly adhering soil particles.

Rhizosphere competence Ability of an organism to colonize the rhizosphere.

Rhizosphere Zone of soil immediately adjacent to plant roots in which the kinds, numbers, or activities of microorganisms differ from that of the bulk soil.

Ribonucleic acid (RNA) Polymer of nucleotides connected via a phosphate ribose backbone, involved in protein synthesis.

Ribosomal RNA (rrna) Types of RNA found in the ribosome; some participate actively in the process of protein synthesis.

Ribosome A cytoplasmic particle composed of ribosomal RNA and protein, which is part of the proteinsynthesizing machinery of the cell.

RNA (ribonucleic acid) A single stranded nucleic acid similar to DNA but having ribose as its sugar and uracil rather than thymine as one of the bases.

RNA processing The conversion of a precursor RNA into its mature form (cutting out the introns).

Root nodule Specialized structure occurring on roots, especially of leguminous plants, in which bacteria fix dinitrogen and make it available for the plant.

Rrna (ribosomal RNA) A class of small and large subunit RNA molecules, coded in the nuclear organizer, that have an integral role in ribosome structure and function (80% of total RNA).

R strategy Ecological strategy where organisms rely on high reproductive rates for continued survival within the community. Populations of r strategists are subject to extreme fluctuations.

Saline soil Soil containing sufficient soluble salt to adversely affect the growth of most crop plants.

Sand Soil particle between 0.05 and 2.0 mm in diameter.

Sanitization Elimination of pathogenic or deleterious organisms, insect larvae, intestinal parasites, and weed seeds.

Saprophyte Nonparasitic nutritional mechanism by which an organism obtains its food exclusively from the degradation of nonliving organic material.

Sclerotium Modified fungal hyphae that form a compact, hard vegetative resting structure with a thick pigmented outer rind.

Secondary metabolite Product of intermediary metabolism released from a cell, such as an antibiotic.

Selective medium Medium that allows the growth of certain types of microorganisms in preference to others. For example, an antibiotic containing medium allows the growth of only those microorganisms resistant to the antibiotic.

Septum (plural, septa) Crosswall (partition) dividing a parent cell into two daughter cells during binary fission or occurring between adjacent cells in hyphae.

Serial dilution Series of stepwise dilutions (usually in sterile water) performed to reduce the populations of microorganisms in a sample to manageable numbers.

Serology Study of antigen antibody reactions in vitro.

Sheath Tubular structure formed around a chain of cells or around a bundle of filaments.

Siderophore Nonporphyrin metabolite secreted by certain microorganisms that forms a highly stable coordination compound (chelate) with iron; a high affinity iron binding compound. There are two major types catecholates and hydroxamates.

Silt Soil particle with a diameter between 0.002 and0.05 mm.

Site (i) In ecology, area described or defined by its biotic, climatic, and soil conditions as related to its capacity to produce vegetation. (ii) Area sufficiently uniform in biotic, climatic, and soil conditions to produce a particular climax vegetation.

Site directed mutagenesis Insertion of a different nucleotide at a specific site in a molecule using recombinant DNA methodology.

Slime layer Diffuse layer of polysaccharide exterior to the cell wall in some bacteria..

Slime mold Nonphototrophic eukaryotic microorganism lacking cell walls, which aggregate to form fruiting structures (cellular slime molds) or simply masses of protoplasm (acellular slime molds).

Soil aggregate Unit of soil structure generally < 10 mm in diameter and formed by natural forces and substances derived from root exudates and microbial products which cement smaller particles into larger units.

Soil atmosphere Gases occupying the pore space in soil. Generally characterized as having a greater percentage of carbon dioxide and a lesser percentage of oxygen than the overlying air.

Soil biochemistry Branch of soil science concerned with enzymes and the reactions, activities, and products of soil microorganisms.

Soil classification See classification.

Soil extract Solution separated from a soil suspension or from a soil by filtration, centrifugation, suction or pressure.

Soil health See soil quality.

Soil horizon Layer of soil or soil material approximately parallel to the land surface and differing from adjacent genetically related layers in physical, chemical, and biological properties or characteristics such as color, structure, texture, consistency, kinds and number of organisms present, and degree of acidity or alkalinity.

Soil microbiology Branch of soil science concerned with soil inhabiting microorganisms and their functions and activities.

Soil organic matter (SOM) Organic fraction of the soil exclusive of undecayed plant and animal residues. Often synonymous with humus.

Soil population (i) All the organisms living in the soil, including plants and animals. (ii) Members of the same taxa.

Soil pore That part of the bulk volume of soil not occupied by soil particles. Soil pores have also been referred to as interstices or voids.

Soil quality Continued capacity of soil to function as a vital living system to sustain biological productivity, maintain the quality of the environment, and promote plant, animal, and human health.

Soil salinity Amount of soluble salts in a soil. The conventional measure of soil salinity is the electrical conductivity of a saturation extract.

Soil science Science dealing with soils as a natural resource on the surface of the earth including soil formation, classification and mapping, and physical, chemical, biological, and fertility properties of soils per se; and these properties in relation to their use and management.

Soil series Lowest category of U.S. system of soil taxonomy; a conceptualized class of soil bodies (polypedons) that have limits and ranges more restrictive than all higher taxa. The soil series serve as a major vehicle to transfer soil information and research knowledge from one soil area to another.

Soil solution Aqueous liquid phase of the soil and its solutes.

Soil structure Combination or arrangement of primary soil particles into secondary particles, units, or peds. The secondary units are characterized and classified on the basis of size, shape, and degree of distinctness into classes, types, and grades, respectively.

Soil texture Relative proportions of the various soil separates in a soil. The major textural classes are sand, silt, and clay.

Soil water potential (total) Amount of work that must be done per unit quantity of pure water in order to transport reversibly and isothermically an infinitesimal quantity of water from a pool of pure water, at a specified elevation and at atmospheric pressure, to the soil water (at the point under consideration). Informally, the amount of energy that must be expended to extract water from soil. The total potential (of soil water) consists of the following gravitational potential, matric potential, and osmotic potential.

Soil (i) Unconsolidated mineral or material on the immediate surface of the earth that serves as a natural medium for the growth of land plants. (ii) Unconsolidated mineral or organic matter on the surface of the earth that has been subjected to and influenced by genetic and environmental factors of parent material, climate (including water and temperature effects), macroorganisms and microorganisms, and topography, all acting over a period of time and producing a product soil that differs from the material from which it is derived in many physical, chemical, biological, and morphological properties, and characteristics.

Solarization Method to control pathogens and weeds where moistened soil in hot climates is covered with transparent polyethylene plastic sheets, thereby trapping incoming radiation.

Southern blot Hybridization of single stranded nucleic acid (DNA or RNA ) to DNA fragments immobilized on a filter.

Spatial variability Variation in soil properties (i) laterally across the landscape, at a given depth, or with a given horizon, or (ii) vertically downward through the soil.

Species In microbiology, a collection of closely related strains sufficiently different from all other strains to be recognized as a distinct unit.

Specific activity Amount of enzyme activity units per mass of protein. Often expressed as micromoles of product formed per unit time per milligram of protein. Also used in radiochemistry to express the radioactivity per mass of material (radioactive and nonradioactive).

Specific epithet Designation of a particular organism in the binomial nomenclature system. For example, coli is the specific epithet of Escherichia coli.

Spermosphere Area of increased microbial activity around a germinating seed.

Spirillum (plural, spirilli) (i) Bacterium with a spiral shape which is relatively rigid. (ii) Bacterium in the genus Spirillum.

Spontaneous Generation The hypothesis that living organisms can originate from nonliving matter.

Sporangiospore Spore formed within a sporangium by fungi in the phylum Zygomycota.

Sporangium Fungal structure which converts its cytoplasm into a variable number of sporangiospores; formed by fungi in the phylum Zygomycota.

Spores Specialized reproductive cell. Asexual spores germinate without uniting with other cells, whereas sexual spores of opposite mating types unite to form a zygote before germination occurs.

Spread plate Method for performing a plate count of microorganisms. A known amount of a serial dilution is spread over the surface of an agar plate. After growth the number of colony forming units is counted.

Stationary phase Period during the growth cycle of a population in which growth rate equals the death rate.

Sterilization Rendering an object or substance free of viable microbes.

Storage polysaccharide Energy reserve deposited in the cell when there is an excess of carbon available. These are usually deposited as large granules in the cell. The most common example of a storage polysaccharide in plants is starch. Its counterpart in animal cells is glycogen.

Strain Population of cells all descended from a single pure isolate.

Structural polysaccharide Polysaccharide that serves primarily as a structural element in cell walls and coats and intercellular spaces, and connective tissue where they give shape, elasticity, or rigidity to plant or animal tissues and protection and support to unicellular organisms. Cellulose is the predominant structural polysaccharide in plant cell walls and chitin is abundant in fungal cell walls and insect exoskeletons.

Structure See soil structure

Substrate (i) Substance, base, or nutrient on which an organism grows. (ii) Compounds or substances that are acted upon by enzymes or catalysts and changed to other compounds in the chemical reaction.

Substrate level phosphorylation Synthesis of high energy phosphate bonds through reaction of inorganic phosphate with an activated (usually) organic substrate.

Substratum a surface within a liquid matrix that can serve as a physical support upon which biofilms can accumulate.

Succession Gradual process brought about by the change in the number of individuals of each species of a community and by the establishment of new species that gradually replace the original inhabitants.

Sulfur cycle Sequence of transformations undergone by sulfur where it is taken up by living organisms, transformed upon death and decomposition of the organism, and converted ultimately to its original state of oxidation.

Surface area Area of the solid particles in a given quantity of soil or porous medium.

Surface soil Uppermost part of the soil, ordinarily moved in tillage, or its equivalent in uncultivated soils ranging in depth from 7 to 20 cm. Frequently designated as the surface layer, the Ap layer, or the Ap horizon.

Symbiosis Living together in intimate association of two dissimilar organisms. The interactions between the organisms can be commensal or mutualistic.

Synergism Association between organisms that is mutually beneficial. Both populations are capable of surviving in their natural environment on their own although, when formed, the association offers mutual advantages.

Syntrophy Interaction of two or more populations that supply each other's nutritional needs.

Systemic Not localized in a particular place of the body; an infection disseminated widely through the body is said to be systemic.

Taxon (plural, taxa) A group into which related organisms are classified.

Taxonomy Study of scientific classification and nomenclature.

Teichoic acids All wall, membrane, or capsular polymers containing glycerophosphate or ribitol phosphate residues.

Teleomorph Sexual stage in reproduction in which cells are formed by the process of meiosis and genetic recombination.

Temperate virus Virus which upon infection of a host does not necessarily cause lysis but whose genome may replicate in synchrony with that of the host.

Terminal electron acceptor External oxidant (often oxygen) that accepts the electrons as they exit from the electron transport chain.

Test Hard external covering or shell.

Texture See soil texture.

Thallus Vegetative body that is not differentiated into tissue systems or organs.

Thermophile Organism whose optimum temperature for growth is between 45 and 85C.

Ti plasmid Conjugative tumor inducing plasmid present in the bacterium Agrobacterium tunefaciens which can transfer genes into plants.

Topsoil (i) Layer of soil moved in cultivation. (ii) The A horizon. (iii) Presumably fertile soil material used to topdress roadbanks, gardens, and lawns.

Toxin Microbial substance able to induce host damage.

Toxin A microbial substance able to induce host damage.

Trace gas Gas other than nitrogen and oxygen in the atmosphere, particularly those gases that are active in the chemistry or radiation balance of the atmosphere.

Transcription Synthesis of an RNA molecule complementary to one of the two strands of a DNA double stranded molecule.

Transcription (L. Trans, across; scrivere, to write) The synthesis of complementary mrna using portions of the sense DNA template (ORF) with the help of RNA polymerase.

Transduction Transfer of host genetic information via a virus or bacteriophage particle.

Transduction Transfer of host genes from one cell to another by a virus.

Transfer RNA (trna) Type of RNA that carries amino acids to the ribosome during translation.

Transformation Transfer of genetic information into living cells as free DNA.

Transgenic Describes genetically modified plants or animals containing foreign genes inserted by means of recombinant DNA techniques.

Translation Synthesis of proteins using the genetic information in mrna as a template.

Transposable element Genetic element that can to move (transpose) from one site on a chromosome to another.

Transposition Movement of a piece of DNA around the chromosome, usually through the function of a transposable element.

Transposon mutagenesis Insertion of a transposon into a gene; this inactivates the host gene leading to a mutant phenotype and also confers the phenotype associated with the transposon gene.

Transposon Transposable element of which, in addition to genes involved in transposition, carries other genes; often confers selectable phenotypes such as antibiotic resistance.

Tricarboxylic acid cycle (TCA cycle, citric acid cycle, Krebs cycle) Series of metabolic reactions by which pyruvate is oxidized completely to carbon dioxide, also forming NADH, which allows ATP production.

Tricarboxylic Acid Cycle see Krebs Cycle.

Trichome Row of cells which have remained attached to one another following successive cell divisions. Trichomes are formed by many cyanobacteria and by species of Beggiatoa.

Trna (transfer RNA) Small cloverleaf RNA molecules that bear specific amino acids (at the 3 end =CCA) to the ribosome during translation; the amino acid is inserted into the growing polypeptide chain when the anticodon of the trna pairs with a codon on the mrna being translated (15%).

Trophic level Describes the residence of nutrients in various organisms along a food chain ranging from the primary nutrient assimilating autotrophs to the predatory carnivorous animals.

Trophic Requirements The movement of energy through an microbial ecosystem is structured according to the primary energy source

Ultramicrobacteria (umb) small (ca 0.3 micrometer), metabolically dormant bacteria produced by starvation. These bacteria produce little or no exopolysaccharide. In the presence of nutrients, the bacteria become active again, regaining normal size, metabolic activity, and eps production.

Uronic acid Class of acidic compounds of the general formula HOOC(CHOH)ncho that contain both carboxylic and aldehydic groups, are oxidation products of sugars, and occur in many polysaccharides; especially in the hemicelluloses.

Vadose zone Unsaturated zone of soil above the groundwater, extending from the bottom of the capillary fringe all the way to the soil surface.

Vector (i) Plasmid or virus used in genetic engineering to insert genes into a cell. (ii) Agent, usually an insect or other animal, able to carry pathogens from one host to another.

Vegetative cell Growing or feeding form of a microbial cell, as opposed to a resting form such as a spore.

Vesicles Spherical structures, formed intracellularly, by some arbuscular mycorrhizal fungi.

Vesicular arbuscular mycorrhiza See arbuscular mycorrhiza.

Viable Alive; able to reproduce.

Viable but nonculturable Organisms that are alive but cannot be cultured on laboratory media.

Viable count Measurement of the concentration of live cells in a microbial population.

Vibrio (i) Curved, rod shaped bacterial cell. (ii) Bacterium of the genus Vibrio.

Virion A virus particle; the virus nucleic acid surrounded by protein coat and in some cases other material.

Viroid A small RNA molecule with viruslike properties.

Virulence Degree of pathogenicity of a parasite.

Virulent V. A virus which lysis or kills the host cell after infection; a non temperate virus.

Virus A genetic element containing either DNA or RNA that is able to alternate between intracellular and extracellular states, the latter being the infectious state.

Water content Water contained in a material expressed as the mass of water per unit mass of oven dry material.

Water potential See soil water potential.

Water retention curve Graph showing soil water content as a function of increasingly negative soil water potential.

Weathering All physical and chemical changes produced in rock by atmospheric agents.

White rot fungus Fungus that attacks lignin, along with cellulose, and hemicellulose, leading to a marked lightening of the infected wood.

Wild type Strain of microorganism isolated from nature. The usual or native form of a gene or organism.

Wilting point See permanent wilting point.

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.

Woronin body Spherical structure associated with the simple pore in the septa separating hyphal compartments of fungi in the phylum Ascomycota.

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.

Yeast Fungus whose thallus consists of single cells that multiply by budding or fission.

Zoospore An asexual spore formed by some fungi that usually can move in an aqueous environment via one or more flagella.

Zygospore Thick walled resting spore resulting from fusion of two gametangia of fungi in the phylum Zygomycota.

Zygote In eukaryotes, the single diploid cell resulting from the union (fusion) of two haploid gametes.

Zymogenous flora Refers to microorganisms, often transient or alien, that respond rapidly by enzyme production and growth when simple organic substrates become available. Also called copiotrophs.