CBE Interdisciplinary Glossary

Microbiology

ADHESION/ATTACHMENT 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.

ANTIBIOTIC A chemical agent that is produced by one organism that is harmful to another organism.

ANTIMICROBIAL AGENT An agent that kills or inhibits microbial growth.

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.

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.

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.

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.

"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.

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.

COLIFORM BACTERIA Members of the genus enterobacteriaceae; described as gram negative, nonsporing facultative rods that ferment lactose with gas formation within 48 hr @ 35^oC. Used as indicator organisms in water and some foods.

Table of Contents

Terms & Concepts by Discipline

Index

COLONY A population of cells growing on solid medium (plates) arising from a single colony forming unit.

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.

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

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

ELECTRON ACCEPTOR A substance that accepts electrons during an oxidation-reduction reaction. Examples for bacteria are oxygen (aerobes), nitrate (nitrate reducing bacteria), and sulfate (sulfate reducers).

ELECTRON DONOR Compound that donates electrons in an oxidation-reduction reaction. Examples are organic carbon and hydrogen.

ENZYME Protein catalyst which drives chemical reactions within a cell. Enzymes display a high degree of specificity with regard to both the substrate on which they act and the type of reaction they catalyze. Enzymes may also be introduced from outside the cell to cause biochemical reactions.

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. (See glycocalyx.)

FACULTATIVE Indicates that a bacterium is able to grow in the presence or absence of an environmental condition (e.g., facultative aerobe).

FLAGELLUM Bacterial cell appendage used for motility.

FLUORESCENT ANTIBODY Immunoglobulin molecule (antibody) coupled with a fluorescent dye.

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. (See EPS.)

GROWTH LIMITING FACTOR That 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.).

Monod Kinetics: Originally spelled "Moe nod kinetics", this term refers to the rate at which one of the Three Stooges could move his head up and down in the "yes" motion.

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.

HETEROGENEITY See Introduction.

HETEROTROPHIC BACTERIA Those bacteria that require an organic carbon source for growth; i.e. derive energy and carbon from organic compounds.

HETEROTROPHIC PLATE COUNT BACTERIA (HPC) Those bacteria that will grow on nonselective heterotrophic medium plates.

INJURY Reversible phenotypic response of bacteria exposed to sublethal stressors.

MINERALIZATION Metabolism of an organic substrate by bacteria to carbon dioxide and water.

PATHOGEN An organism capable of producing disease in a host.

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.

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.

SUBSTRATE A molecule undergoing reaction with an enzyme. Any one of a number of essential nutrients for microbial growth. Specific substrates vary with specific physiology of microorganisms (bacteria or eukaryotic cells).

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.

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

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.