DEFINITIONS OF MICROBIOLOGICAL TERMS, GLOSSARY
These terms are given in alphabetic order to allow the reader to more easily find the terms of interest later. Note that the terms are also listed in the index.
Acidotrophic bacteria, bacteria which are able to flourish in very acidic (pH <3.5) conditions. Many are aerobic and function over relatively narrow pH ranges.
Adaptability, the ability of microorganisms either as individual strains, or as a consortium of strains, to adapt to function in some way within a given environment. Often there is a lag (induction) time before this activity commences.
Aerobic microorganisms, microbes which can function using oxygen in their respiratory activities.
Aggressivity, the state in which an organism is active in its environment and able to compete with other strains for space, nutrients, water and gases.
Anaerobic microorganisms, microbes which are able to function in the presence of oxygen. For many of these organisms, they are able to function using oxygen when available (facultative anaerobes) while other strains cannot function in the presence of oxygen which is toxic to them (strictly anaerobic). There are a very few strict anaerobes which are not sensitive to the toxic effects of oxygen. These are known as aerotolerant.
Archaebacteria, are a group of bacteria which evolved very early on the in the evolution of the planet. These bacteria are now found populating some of the extreme environments (eg, highly saline, sulfur-rich, methane generating and high temperatures).
Attachment, the act of a bacteria or a biocolloid becoming fixed to a surface. Growth may then follow leading to the formation of biofilms.
Bacteriophage, a virus which infects bacteria and multiplies within the cells. Usually a bacteriophage can only infect a limited range of bacterial strains.
BARTTM, a patented biological activity reaction test biodetection system which can be customised to determine the aggressivity and composition of selected consortia of microorganisms.
BCHTTM, a patented blended chemical heat treatment system which can be applied to rehabilitate biofouled water wells and systems by a tri-phasic technology.
Bioaccumulator, a biological entity which is able to accumulate (either actively for degradation, or passively) chemicals within the surface coatings of EPS or within the cells themselves.
Bioamplifier, an organisms which is able to catalyze a particular physical and/or chemical event causing the event to occur at an accelerated rate.
Biocides, specific chemicals or compounds which have a deleterious impact on the targeted organism.
Biocolloid, a buoyant particle which is composed mostly of water bound together by EPS and populated by some microorganisms. Sizes may range from 6 to 100 microns or more in diameter. These suspended particles are also found to be able to act as bioaccumulators.
Biodegradation, the act of degrading a molecule to one or more smaller molecules by biochemical mechanisms (eg, enzyme action).
Biodetector, an instrument, device or mechanism by which the presence of biological activity can be determined.
Biofilm, an slime-like matrix composed of EPS within which a consortium of microorganisms flourish. These biofilms may either grow over surfaces, or occupy voids in a porous medium.
Biofouling, any deleterious event in which a definable biological activity causes a deterioration in and engineered or natural process or system. Deleterious effects range from clogging, corrosion, and plugging to gas production and bioaccumulation.
Bioincumbancy, the fraction of the volume within a biocolloid or biofilm occupied by viable cells.
Biomass, the mass of a living entity which may be expressed as either the wet or dry weight. Biomass may furthermore be given as the total mass including all associated mass; or as the viable mass which would include just the viable cells. In biofilms, the total mass would relate to the total weight of the "slime" as such while the viable mass would include just the mass directly associable with the living cells.
Biosensor, a device or methodology which utilises the shift in a targeted signal (commonly electro-magnetic) to quantify a biological activity or presence.
Biozone, a localized site where a specific form of microbial consortium can be located.
Clogging, the generation of a mass which interferes with physical functioning (eg, hydraulic conductivity) of a porous medium (eg, gravel pack, sand filter). Clogging can be formed through the maturation of biofilms fouling the media and may become complex in structure.
Clogging Risk Index (CRI), a factorial presentation of the likelihood of a significant clogging occurring within a defined system.
Coliform bacteria, the presence of these bacteria is generally regarded as being indicative of an increased hygiene-risk because of the potential for faecal contamination. The coliform bacteria are abundant in the faeces of warm blooded animals and Escherichia coli is particularly common in the human species. Generally, the coliform bacteria do not survive long in natural waters and so form a good indicator organisms for recent (significant) pollution of raw or partially treated sewage.
Colony Forming Units (cfu), when microorganisms do grow on agar media they commonly form visible distinguishable structures composed mainly of cellular material which are called colonies. Each of these colonies is considered to have formed from a single colony forming unit which may be a single cell or a clump of cells. By appropriate mathematical relationships of the dilution of the sample and the area of the agar inoculated, it is possible to predict a population as either cfu/ml (for liquids), cfu/g (for solids) or cfu/cm2 (for surfaces).
Corrosion, the process of erosive deterioration in the physical form and engineered characteristics of a structure. These processes frequently involve electrolytic and/or corrosive chemical (eg, acids) effects which are sometimes mediated by microbial activities. It has been observed that corrosive pitting can form directly under biofilms.
Culture, (verb) the act of successfully growing a unique strain or a consortium of microorganisms; (noun) a viable collection of a single strain of microorganisms which has been selectively grown.
Denitrification, the process of reducing nitrate via nitrite to nitrogen gas by bacterial action. There are four stages in this process. In water which has become polluted with sources of organic nitrogen (eg, sewage or septic waste) and then been subjected to aerobic (oxidative) nitrification, nitrates are a major product. If conditions now become anaerobic, these accumulating nitrates are reduced by denitrification.
Disinfection, the act of destroying by chemical and/or physical means microorganisms that are causing an undesirable infestation at a site. It does not mean that all microorganisms are killed, it means that there is a selective action.
Encrustation, a relatively solid plate-like or crystalline structure coating a surface. It appears to be chemical in nature due to the hardness of the structure. Often brittle (when dry) or plastic (when wet), the organic content is usually relatively small.
EPS or extracellular polymeric substances, many microorganisms do produce an "overcoat" of polymers outside of the cell. These polymers bind water and various chemicals to form protective and storage functions.
Eutrophic conditions, these occur when there is an abundance of nutrients and the microorganisms are able to grow to form a large biomass. A rapidly clogging well due to IRB growth could be considered as being eutrophic.
Fringe Effects, the zone wherein the treatment is marginalized and therefore has a lesser of different impact.
Gallionella, is a well known iron related bacterium which is easily recognized by the long often twisted ribbon-like tail they produce. This tail often will break off and be carried with the water flow.
gRAM Stain, is a standard staining procedure which is frequently used as one of the first stages in the identification of bacteria into gRAM negative and gRAM positive types.
Halotrophs, microorganisms able to survive and grow in brine solutions. Some of these organisms cannot even survive when the salt concentration is less than 12%.
Heterotrophic microorganisms, those microbes which obtain their energy from the breaking down of organic material. Some of these microbes are very specialised (eg, cellulose degraders) while other can utilize a variety of organic compounds.
Hydrolysis, the act degrading complex molecules (eg, polymers) into smaller molecules through the addition of H2O.
Incubation, the act of growing an organism under conditions that will encourage rapid growth (compared to natural conditions).
Induction period, the period of adaptation that an organism has to pass through before it is able to flourish in a favorable habitat.
Infiltration, the act of a material or organism passaging into a porous medium.
In situ, at site.
Invasiveness, the ability of an organism to enter into an environment and function at some level from survival to growth.
In vitro, under controlled (laboratory) conditions.
Iron oxidising bacteria, those bacteria able to oxidise iron by any means from a reduced form of iron (ferrous form) to an oxidised (ferris) state.
Iron reducing bacteria, those bacteria which are able to reduce iron by any means from an oxidised form (ferric) to a reduced (ferrous) state.
Iron related bacteria (IRB), all of those bacteria which are able to accumulate iron in another form beyond that for basic metabolic functioning. These accumulated iron compounds generally collect within the slime (EPS) around the cells and gradually harden (crystallise) over time.
Limiting nutrient, a major nutrient which is in short supply and restricts the growth of a biomass. Limitations could also be created by the limiting nutrient distorting the ratios of nutritional elements outside of range that would support growth.
Macrofouling, an intense and/or widespread form of biofouling.
Magnetotactic bacteria, are a group of bacteria which actually possess "biocompasses" (called magnetosomes). These bacteria are able to orient themselves within electromagnetic fields.
Marginal clogging, where there is less than a 20% loss in production capacity but a water well shows symptoms of being clogged, then this phenomenon is considered marginal but discernable.
Mechanical disruption, the use of physical methods (such as freezing, ultrasonics, pressure pulses, radical thermal gradients) to disrupt a biofouling event.
Membrane filtration (MF), the use of a non-absorbent porous membrane to trap particles (including bacteria) which allow the water to filter through. It is a technique used to enumerate low numbers of bacteria in water by concentration the cells on the filters surface where they may be grown to form visible countable colonies. Pore sizes commonly employed are of 0.22 and 0.45 microns diameter.
Mesotroph, an organism which will grow over a temperature range somewhere between 15 and 15oC.
Microbial growth potential (MGP), the theoretical growth which may be expected to occur within a defined environment utilising the available nutrients.
Microcosm, a habitat within which there is little diversity in the organisms present or the environmental factors. Often applied to laboratory simulations of "real world" situations (eg, well microcosm used to simulate clogging processes in wells).
MPN most probable number, some microbiological techniques to determine populations use a statistical projection of the population as the most probable number and do not specifically count the individual cells as such.
Negative staining, sometimes bacteria are easy to stain due to the fuzzy EPS around the cell. One alternative is to stain the background so that the cell (and its EPS slimes) can be more easily viewed microscopically.
Nitrification, this biological conversion of ammonium to nitrate occurs under oxidative (aerobic) conditions and is a major part of the nitrogen cycle.
Nitrogen fixation, the act of a biological system fixing nitrogen usually as ammonium (as the intermediary). Some microorganisms under stress through an inadequate nitrogen resource for growth can fixate nitrogen.
Nosocomial, term used for microorganisms which are normal inhabitants of a natural environment but can, under certain circumstances, cause infections in warm blooded animals including man.
Occlusion, the reduction of hydraulic conductivity (flow) through a porous medium as a result of the growth of a clogging structure which is now occupying a significant void volume.
Oligotrophic conditions, these occur where there are few nutrients in the system and the microorganisms are not able to grow to form a significant biomass.
Particulates, suspended material in water, may be inorganic and/or organic in nature. May contain living microorganisms and be colloidal in structure (biocolloid).
Pasteurization, the process of applying heat to a sufficient extent to retard or destroy a recognized nuisance microbial population. Usually involves the application of heat to a minimum of 40oC above the ambient temperature for the system.
Planktonic, references microorganisms able to grow while suspended independently in water.
Plugging, see clogging.
Preventative Maintenance (PM), a management strategy to allow the ongoing monitoring of a system or process to ensure that there is a reactive scenario in place to control an form of recognized deterioration.
Pseudomonad bacteria, are gRAM negative aerobic bacteria which frequently dominate in waters polluted with specific organics. Some strains are nosocomial pathogens.
Recalcitrant, a chemical which does not degrade, is stable and does persist within the environment.
Rehabilitation, the returning of a well or other system to its original specified state by the application of suitable treatments.
Reinfection, the act of an infestation becoming reestablished within a system or process.
Sessile, organisms that are attached to a surface either directly or indirectly.
Shock treatment, the application of a higher than normal dose in order to maximize the effectiveness of the treatment being applied.
Slime, a surface growth on, or originating from, a surface which may be jelly-like if form. Such slimes are usually infested with various microorganisms and can act as sites for the bioaccumulation of various chemicals.
Slime Forming Bacteria (SLYM), bacteria which do produce slimes (from EPS) but do not necessarily accumulate iron within these slimes.
Sloughing, the act of a slime, for whatever reasons, breaking up and releasing particles (from the slime) to the water passing over the slime.
Spreadplate, name given to the microbiological procedure for enumerating microorganisms through their ability to form colonies on selected agar media when dispersed ("spread") over the agar surface and incubated.
Sulfate Reducing Bacteria (SRB), anaerobic bacteria which able to reduce sulfate to hydrogen sulfide. This event may initiate electrolytic corrosion and/or rotten egg taste and odors in water.
Thermal Death Point, the lowest temperature that is required to destroy a specific strain or consortium of microorganisms in ten minutes.
Thermotroph, an organisms which is able to grow at temperatures in excess of 45oC.
Total Nitrogen, the total amount of nitrogenous compounds determined to be in the water exclusive of nitrogen (N2) itself. Major fractions include nitrate - N, nitrite - N, ammonium - N and Kjeldahl nitrogen.
Total Organic Carbon, the total amount of organic carbon in the sample. May include soluble and particulate forms which may, or may not be, recalcitrant.
Total Phosphorus, the total amount of phosphorus detected in the sample. May be four forms: soluble inorganic phosphorus, SIP; soluble organic phosphorus, SOP; particulate inorganic phosphorus, PIP; and particulate organic phosphorus, POP.
Tubercles, these are raised encrustations often incorporating rusty flakes. They commonly grow on surfaces and form the sites for enhanced electrolytic corrosion. Biofilms are often generated within the tubercle.
Tyndallization, the act of repeating a treatment sequentially in order to destroy the survivors of the previous treatment as they grow and become more vulnerable to treatment process. Commonly the treatment are performed three time with a sufficient interval in between to allow the survivors to grow.
Ultramicrobacteria (UMB), very small electrically neutral microorganisms which are in a state of suspended animation. They are able to survive in this form for very long periods of time and recover when they are exposed to a favorable environment.
Viable units, a form of measuring the number of microorganisms in terms of their viable (detectable) units which may consist of one or mor cells.
Wolfe's medium, a specialized medium widely used for the selective growth of Gallionella.
WR medium, a modified Winogradsky's medium used to determine the presence and numbers of iron related bacteria.
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