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

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

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

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

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

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

acid soil- Soil with a pH value < 6.6.

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

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

active site- Region of an enzyme where substrates bind.

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

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

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

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

agar- Complex polysaccharide derived from certain marine algae that is a gelling agent for solid or semisolid microbiological media. Agar consists of about 70% agarose and 30% agaropectin. Agar can be melted at temperature above 100¼C; gelling temperature is 40-50¼C.

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.

anabolism- Metabolic processes involved in the synthesis of cell constituents from simpler molecules. An anabolic process usually requires energy.

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.

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.

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.

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.

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.