Microbiology: Key Terms and Glossary

An aerated suspension of bacteria and grazing protozoa that oxidises the organic load of wastewater, then settles so that part of the biomass can be returned.

Able to grow in air by fermentation, without respiring oxygen; the usual enzyme picture is superoxide dismutase without catalase.

Reduction of microbes on living tissue, as distinct from treatment of an inert surface.

A non-photosynthetic plastid of algal ancestry in apicomplexan parasites, which human cells do not have.

A sexual fungal spore formed inside an ascus.

A vessel that holds saturated steam under pressure so the steam can rise above the ordinary boiling point of water. The pressure is how the temperature is raised; it is not itself the killing agent.

The light-harvesting pigment of classical anoxygenic phototrophs, which do not take electrons from water and do not release oxygen.

The nitrogen-fixing form of a rhizobium inside a plant-derived membrane in a nodule.

A grouping of viruses by genome type and by what must happen before a host ribosome can translate viral mRNA.

A sexual fungal spore formed on a basidium.

An enzyme that opens the beta-lactam ring and thereby inactivates that class of antibiotic.

Addition of microorganisms to a contaminated site, which helps only if they actually meet the pollutant.

The dissolved oxygen that microbes would consume in oxidising the organic matter present in a water.

A surface-associated community in which slow growth and poor penetration let cells survive treatments that kill the same strain once it is dispersed.

Supply of something residents lack, such as a nutrient or an electron acceptor, so that they can degrade a pollutant already present.

The number of infectious particles released from one infected cell.

The protein shell that encloses a viral genome.

An organised polysaccharide layer outside the cell that can aid attachment, resist drying, and hinder phagocytosis.

The minimum, the optimum, and the maximum temperature at which a given organism grows.

Presence of a pathogenic organism in a person who is not ill, so the organism is not confined to cases of disease.

An enzyme that converts hydrogen peroxide to water and oxygen.

An organism that draws energy from oxidising an inorganic electron donor and takes its carbon from carbon dioxide.

An organism that takes energy, electrons, and carbon from organic compounds.

A continuous culture, fed and emptied at the same rate, that holds specific growth rate equal to the dilution rate until the culture washes out.

The β-1,4 polymer of N-acetylglucosamine that stiffens the fungal cell wall.

Transformation of a molecule the cell does not use as food, which need not remove its harm and can increase it.

Multiplication of a microbe on a host without damage to that host.

The obstacle that an established microbiota sets against a newcomer by occupying the available niches.

A visible mass of microbial growth on a solid surface, taken as evidence of descent from one progenitor but not as proof of purity.

An asexual spore of many ascomycete fungi, produced as a means of dispersal rather than as a single dormant copy of one cell.

A resistant, non-feeding stage in which some protozoa are transmitted.

The host in which a parasite’s sexual reproduction takes place; for *Plasmodium*, the female *Anopheles*.

Anaerobic respiration that reduces nitrate all the way to N2. Reduction that stops at nitrite, as in *E. coli*, is not this process.

The volume of medium flowing through a culture in a unit of time, divided by the culture volume, equal at chemostat steady state to the specific growth rate.

A compound, accumulated with calcium in the endospore core, that is part of the dehydrated state resisting heat.

Killing or inhibiting pathogens on an inert surface. Endospores often remain, and the agent is not meant for living tissue.

Antigenic change in influenza from point mutations in the surface glycoproteins, so that antibody to an earlier surface fits the new one less well.

The interval in which the infecting particle has been taken apart and no infectious progeny yet exist.

Active export of an antimicrobial from the cell, which can confer resistance by keeping the internal amount low.

A dormant, non-dividing cell formed inside a vegetative bacterium, with a dehydrated core that survives heat lethal to the growing cell. It is not a reproductive fungal spore.

Lipid A of the Gram-negative outer membrane: heat-stable, encoded on the chromosome, and a trigger of widespread inflammation rather than of one catalytic lesion.

Host membrane, studded with viral glycoproteins, wrapped around some virions and required intact if those particles are to remain infectious.

An archaeal membrane lipid in which isoprenoid chains are joined to glycerol by ether bonds, with stereochemistry opposite to bacterial ester lipids.

A protein poison released by a bacterium, often from a phage or plasmid gene, usually destroyed by heat and specific in what it attacks.

In the oxygen classes of these notes, able to grow without oxygen and able to grow better when oxygen is available.

An energy metabolism that restores NAD+ by reducing an organic product of the substrate, with ATP only from substrate-level phosphorylation.

The protein subunit of the bacterial flagellar filament, a rigid helix turned by a rotary motor rather than a bending cilium.

The sexual stage of *Plasmodium* formed in the human, which does not multiply there and becomes gametes in the mosquito.

The interval between successive divisions while a population is growing exponentially. The doubling relation does not describe lag, stationary phase, or death.

The claim that particular microbes cause particular fermentations and infectious diseases, rather than life appearing of itself in broth or disease arising only as a miasma.

An organic molecule the cell cannot make, such as a vitamin, an amino acid, or a base, and which must therefore be supplied.

The influenza glycoprotein that binds sialic acid and later fuses viral and host membranes.

Protection of people who are still susceptible because immunity already present stops chains of transmission from keeping themselves going. These notes do not convert that idea into a percentage for any disease.

A thick-walled cell along some cyanobacterial filaments that turns off oxygenic photosystem II and so gives nitrogenase a low-oxygen place to work.

A fermentation whose product is essentially lactate alone.

Movement of genes between organisms other than from parent to offspring, by conjugation, transduction, or transformation, which can carry resistance into a species that never encountered the drug.

A tubular fungal filament that grows at its tip.

A dormant liver stage, formed by *Plasmodium vivax* and *Plasmodium ovale* but not by *Plasmodium falciparum*, that can resume long after the blood cycle.

An organism, such as *E. coli*, whose presence is read as a sign of faeces, not as the pathogen of concern and not as a proxy for viruses or for chlorine-resistant cysts.

The HIV enzyme that inserts reverse-transcribed viral DNA into a host chromosome, leaving a provirus that persists.

Historical criteria that an organism be found in each case, grown in pure culture, able to reproduce the disease from that culture in a susceptible host, and isolated again. Carriage, failure to grow on lifeless media, and toxin already formed in food are limits where that chain does not hold.

The opening phase of a closed culture, before exponential increase, while cells prepare by making enzymes, repairing, or germinating.

The time from infection until the first infectious progeny are free outside the cell.

A plant haem protein in the legume nodule that keeps free oxygen low beside nitrogenase while still allowing the bacteroids a supply for respiration.

A symbiosis of a fungus with a green alga or a cyanobacterium, not one species.

The acylated, membrane-embedded disaccharide of lipopolysaccharide, which is the toxic portion called endotoxin.

An enzyme that cuts the β-1,4 bond between the amino sugars of peptidoglycan.

The *Plasmodium* stage released from a schizont that enters red blood cells.

Archaeal energy metabolism that yields methane from carbon dioxide plus hydrogen, or from acetate.

An organism studied here as a single cell, a filament, or a non-cellular infectious particle, usually too small to resolve by eye. The word names a way of working, not one clade.

A fermentation that yields several acids, and often ethanol and gas from formate, rather than a single end product.

Tests that a gene be associated with pathogenic strains, that disrupting it reduce virulence, and that putting it back restore virulence. Two factors that can replace each other, or a gene that cannot be deleted, can hide a real contribution from this test.

A very long branched hydroxy fatty acid of the acid-fast wall, which makes that wall waxy and hard for many chemicals to cross.

A root–fungus symbiosis in which the fungus obtains plant carbon and the plant obtains mineral nutrients.

The influenza enzyme that cleaves sialic acid and so releases new particles from the cell that made them.

Oxidation of ammonia to nitrite and of nitrite to nitrate by chemolithotrophs.

The enzyme that reduces N2 to ammonia, and that is inactivated if oxygen reaches it.

The region of a bacterial or archaeal cell that holds the chromosome, without a surrounding nuclear membrane.

The variable outer polysaccharide of lipopolysaccharide, whose repeats distinguish O serotypes.

The motile zygote of *Plasmodium* in the mosquito, which moves from the gut contents to form an oocyst.

A filamentous stramenopile with cellulose and glucan walls and diploid vegetative growth, similar to a mould in shape but not a fungus.

A microbe that causes disease only when a host defence is already breached.

Heat treatment that reduces pathogens or spoilage organisms in a product while stopping short of sterilisation, so endospores can survive it.

An enzyme that cross-links peptidoglycan and is inactivated when a beta-lactam acylates it.

The bacterial wall polymer of alternating amino sugars in β-1,4 linkage, cross-linked by short peptides, which bears the turgor of the cell.

A dormant cell in a population that survives a cidal drug and later produces daughters that are again susceptible.

An organism that uses light for energy, an inorganic compound for electrons, and carbon dioxide for carbon.

A thin protein filament used for sticking to a surface and, in particular forms, for twitching, DNA uptake, or holding cells together during conjugation.

A usually circular DNA molecule, smaller than the chromosome and dispensable, that often carries resistance, a virulence factor, or a catabolic pathway.

Poison made in a food before the food is eaten, so illness does not require the organism to colonise the person.

A product made during growth and tied to central metabolism.

A microbe that can damage a host whose defences were intact.

A phage genome inserted in the bacterial chromosome and copied with it.

In these notes, the HIV enzyme that cuts the polyproteins of a newly released particle so the capsid can condense.

The electrochemical gradient of protons across a membrane, built in bacteria and archaea at the plasma membrane and used for ATP synthesis and other work.

A wall polymer of some methanogens that resembles peptidoglycan but is β-1,3 linked and lacks the peptide target of lysozyme and of beta-lactams.

A population taken to descend from one cell or one colony-forming unit, so that a property can be credited to one kind of organism. The term is an argument about descent, not a recipe for a medium.

The people, animals, or habitat in which a pathogen maintains itself over time, which need not be the immediate source of a given case.

The retroviral enzyme that copies the RNA genome into DNA.

A protein or glycoprotein lattice that forms the wall of many archaea.

Lowering of a microbial load, often on equipment that touches food, to a level a public-health standard accepts. Sanitised is not sterile.

A product made after growth slows and not required for central metabolism; in these notes antibiotics are the example.

A large antigenic jump in influenza A when genome segments from two viruses reassort and a new surface glycoprotein meets a population without matching immunity.

The *Plasmodium* stage, from the mosquito’s salivary glands, that invades a liver cell.

Destruction or removal of all viable life, including bacterial endospores and viruses.

Restraint in antimicrobial use so that a drug is not applied where it has no target and is not spent only on selecting resistance in the resident microbiota.

Direct transfer of a phosphoryl group from a metabolic intermediate to ADP, without a membrane respiratory chain.

An enzyme that converts superoxide to hydrogen peroxide and oxygen.

Pasteur’s vessel, still open to the air, whose bent neck trapped dust and so kept boiled infusion clear until that dust was washed back in.

A partnership in which one organism’s fermentation remains energetically favourable only because a partner removes a product such as hydrogen.

An exotoxin spoiled as a catalyst but still recognisable as an antigen.

The active, feeding form of a protozoan, as distinct from a cyst.

A bacterial injectisome, related to the flagellar base, that delivers proteins into a host cell.

An organism that cannot be grown on lifeless media, so the pure-culture step of Koch’s chain cannot be carried out in that form.

A complete extracellular virus particle: a genome inside a capsid, sometimes also inside a membrane, with no metabolism and no ribosomes of its own.

A small circular single-stranded RNA of plants that has no capsid and encodes no protein.

A microbial component whose loss makes disease less severe or less likely.

The vapour pressure of water in a material divided by that of pure water. Lowering it can stop growth, but it does not sterilise.

A fungus that grows as a single cell rather than as a mycelium.

A human infection whose maintaining reservoir is in other animals.