C

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.

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- 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.

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.

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

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

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

chemoorganotroph- Organism that obtains energy and electrons (reducing power) 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.

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.

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- Gram-negative, nonspore-forming facultative rod that ferments lactose with gas formation with 48 hours at 35¼C. 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.

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

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.

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.

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

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.

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.

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

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- Selectively permeable membrane surrounding the cell's cytoplasm.