Hogg S. Essential microbiology
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428 GLOSSARY
Benthic zone the sediment of mud and organic matter at the bottom of a pond or
lake.
Beta-lactamase an enzyme that breaks a bond in the β-lactam core of the penicillin
molecule.
Bioaugmentation the deliberate introduction of specific microorganisms into an
environment in order to assist in bioremediation.
Biochemical oxygen demand (BOD) the amount of oxygen needed by
microorganisms to oxidise the organic content of a water sample.
Biodegradation the natural processes of breakdown of organic matter by
microorganisms.
Biodeterioration the damage caused to materials of economic importance due to
biological (mainly microbial) processes.
Biofilm a complex system of microorganisms and their surrounding polysaccharide
matrix.
Biomass the total amount of cellular material in a system.
Bioreactor a fermentation vessel for the controlled growth of microoganisms.
Bioremediation the use of biological processes to improve a specific environment,
such as by the removal of a pollutant.
Calvin cycle a pathway for the fixation of carbon dioxide, used by photosynthetic
organisms and some chemolithotrophs.
Capsid the protein coat of a virus particle.
Capsomer a protein subunit of a viral capsid.
Capsule a clearly defined polysaccharide layer surrounding the cell of certain
procaryotes.
Carcinogen an agent capable of causing cancer.
Catabolism those reactions that break down large molecules, usually coupled to a
release of energy.
Catabolite repression the mechanism by which the presence of a preferred nutrient
(generally glucose) has the effect of preventing the synthesis of enzymes that
metabolise other nutrients.
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GLOSSARY 429
Central Dogma of biology the proposal that information (= genetic) flow in
organisms is in one direction only, from DNA to RNA to protein.
Centromere the central region of the chromosome that ensures correct distribution
of chromosomes between daughter cells during cell division.
Chemotroph an organism that obtains its energy from chemical compounds.
Chloroplast a chlorophyll-containing organelle found in photosynthetic eucaryotes.
Chromosome a nuclear structure on which most of a eucaryotic cell’sgenetic
information (DNA) is carried, in association with specialised proteins called histones.
The nucleoid of procaryotes (q.v.) is also often referred to as a chromosome.
Cilium (pl. cilia) a short motile hair-like structure found on the surface of some
eucaryotic cells.
Citric acid cycle see Tricarboxylic acid cycle.
Clamp connection a mechanism, unique to members of the Basidiomycota, for
ensuring the maintenance of the dicaryotic state.
Cloning the production of multiple copies of a specific DNA molecule. The term is
also used to describe the production of genetically identical cells or even organisms.
Coccus (pl. cocci) a spherically-shaped bacterium.
Codon a sequence of three nucleotide bases that corresponds to a specific amino
acid.
Coenocytic containing many nuclei within a single plasma membrane.
Coenzyme a loosely-bound organic cofactor that influences the activity of an
enzyme.
Cofactor a non-protein component of an enzyme (often a metal ion) essential for its
normal functioning.
Commensal an organism that lives in or on another organism, deriving some benefit
from the association but not harming the other party.
Commensalism an association between two species from which one participant
(the commensal) derives benefit, and the other is neither benefited nor harmed.
Competence (of a bacterial cell): the state of being able to take up naked DNA
from outside the cell.
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430 GLOSSARY
Compound a substance comprising the atoms of two or more elements.
Conidiophore an aerial hypha that bears conidia.
Conidium (conidiospore) an asexual spore, found in members of the Ascomycota
and Actinomycetes. Often forms chains.
Conjugation a process of genetic transfer involving intimate contact between cells
and direct transfer of DNA across a sex pilus.
Consumer a heterotroph that derives energy from the consumption of other
organisms.
Continuous culture a microbial culture in which nutrient concentrations and other
conditions are kept constant by the addition of fresh medium and the removal of old.
Contractile vacuole a fluid-filled vacuole involved in the osmoregulation of certain
protists.
Cosmid a hybrid cloning vector capable of accommodating inserts of up to 50kb.
Covalent bond a bond formed by the sharing of a pair of electrons between atoms.
Cyanobacteria a group of mostly unicellular procaryotes that carry out oxygenic
photosynthesis. Commonly known as the blue-greens.
Decimal reduction time (D value) the time needed to reduce a cell population by a
factor of ten (i.e. to kill 90% of the population) using a particular heat treatment.
Decomposer an organism that breaks down the remains and waste products of
producers and consumers.
Defined medium a medium whose precise chemical composition is known.
Denitrification the reduction, under anaerobic conditions, of nitrite and nitrate to
nitrogen gas.
Diauxic growth a form of growth that has two distinct phases due to one carbon
source being used preferentially before a second.
Dicaryon a structure formed by two cells whose contents, but not nuclei, have
fused.
Differential medium a medium that allows colonies of a particular organism to be
differentiated from others growing in the same culture.
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GLOSSARY 431
Differential stain a stain that employs two or more dyes to distinguish between
different cellular structures or cell types.
Dimorphic existing in two distinct forms.
Dioecious having male and female reproductive structures on separate individuals.
Diploid having two sets of chromosomes.
Disaccharide a carbohydrate formed by the joining of two monosaccharides.
Disc diffusion method a method for assessing the antimicrobial properties of a
substance.
Disinfection the elimination or inhibition of pathogenic microorganisms in or on an
object so that they no longer pose a threat.
Dissimilatory sulphate reduction the reduction of sulphate to hydrogen sulphide by
obligate anaerobes, using either an organic compound or hydrogen gas as electron
donor.
DNA library a collection of cloned DNA fragments.
Domain the highest level of taxonomic grouping.
Eclipse period the stage of a viral replication cycle in which no complete viral
particles are present in the infected host cell.
Ecosystem the organisms of a particular habitat, together with their inanimate
surroundings.
Ectoparasite a parasite that attaches to the outside of its host.
Electron a subatomic particle carrying a negatively charge.
Electron transport chain a series of donor/acceptor molecules that transfer electrons
from donors (e.g. NADH) to a terminal electron acceptor (e.g. O
2
).
Embden Meyerhof pathway see Glycolysis.
Endoparasite a parasite that fully enters its host and lives inside it.
Endoplasmic reticulum a tubular network found in the cytoplasm of eucaryotic cells.
Endospore a highly resistant spore found within certain bacteria.
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432 GLOSSARY
Enrichment culture a culture that uses a selective medium to encourage the growth
of an organism present in low numbers.
Entner-Doudoroff Pathway an alternative pathway for the oxidation of glucose,
producing a mixture of pyruvate and glyceraldehyde-3-phosphate.
Enzyme a cellular catalyst (usually protein), specific to a particular reaction or group
of reactions.
Epiphyte an organism that grows on the surface of a plant.
Eucaryote an organism whose cells contain a true nucleus and membrane-bound
organelles such as mitochondria and endoplasmic reticulum.
Excision repair a repair mechanism in which damaged sections of DNA are cut out
and replaced.
Exon a coding region of a gene. c.f. intron
Expression vector a vector that allows the transcription and translation of a foreign
gene inserted into it.
Facilitated diffusion the transport of molecules across a membrane with the help of
carrier proteins. Transport takes place down a concentration gradient, and energy is
not required.
Facultative anaerobe an organism that can grow in the absence of oxygen, but
utilises it when available.
Fastidious (of an organism): unable to synthesise a range of nutrients and therefore
having complex requirements in culture.
Fatty Acid a long-chain hydrocarbon chain with a carboxyl group at one end.
Feedback inhibition a control mechanism whereby the final product of a metabolic
pathway acts as an inhibitor to the enzyme that catalyses an early step (usually the
first) in the pathway.
Fermentation a microbial process by which an organic substrate (usually a
carbohydrate) is broken down without the involvement of oxygen or an electron
transport chain, generating energy by substrate-level phosphorylation
Flagellum a long hair-like extracellular structure associated with locomotion. Found
in both procaryotes and eucaryotes, although each has its own distinctive structure.
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GLOSSARY 433
F plasmid a plasmid containing genes that code for the construction of the sex pilus,
across which it is transferred to a recipient cell.
Frameshift mutation a mutation that results in a change to the reading frame, and
thus an altered sequence of amino acids downstream of the point where it occurs.
Fungi a kingdom of non-photosynthetic eucaryotes characterised by absorptive
heterotrophic nutrition.
Gamete a haploid reproductive cell arising from meiosis. Fuses with another gamete
to form a diploid zygote.
Gametophyte the haploid, gamete-forming stage in a life cycle with alternation of
generations.
Gene a sequence of DNA that usually encodes a polypeptide.
Generalised transduction the transfer of a gene from one bacterial cell to another
as a result of being inadvertently packaged into a phage particle.
Generation (doubling) time the time taken for a population of cells to double in time
under specific conditions.
Genetic code the 64 triplet codons and the corresponding amino acids or
termination sequences.
Genome the complete genetic material of an organism.
Genotype the genetic make-up of an organism.
Gluconeogenesis a series of reactions by which glucose is synthesised from
compounds such as amino acids and lactate.
Glycolysis a series of reactions by which glucose is oxidised to two molecules of
pyruvate with the synthesis of two molecules of ATP.
Glycosidic linkage a covalent linkage formed between monosaccharides.
Golgi apparatus an organelle of eucaryotes, comprising flattened membranous
sacs.
Gram stain a differential stain that divides bacteria into Gram-positive (purple) or
Gram-negative (pink). The reaction depends on the constitution of the organism’scell
wall.
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434 GLOSSARY
Group translocation a form of active transport in which a solute is modified to
prevent its escape from the cell.
Haploid having only one set of chromosomes.
Haloduric able to tolerate high salt concentrations.
Halophilic showing a requirement for moderate to high salt concentrations.
Heterotroph an organism that must use one or more organic molecules as its source
of carbon.
Hexose a six-carbon sugar.
Hexose monophosphate shunt see Pentose phosphate pathway
Hfr cell a bacterial cell that has a transferred F plasmid integrated into its
chromosome.
Histone a basic protein found associated with DNA in eucaryotic chromosomes.
Horizontal transfer the transfer of genetic material between members of the same
generation.
Human genome project an international effort to map and sequence all the DNA in
the human genome. The project has also involved sequencing the genomes of
several other organisms.
Hydrogen bond a relatively weak bond that forms between covalently
bonded hydrogen and any electronegative atom, most commonly oxygen or
nitrogen.
Hydrophilic (‘water-loving’):having an affinity for water.
Hydrophobic (‘water-hating’):repelled by water.
Hypha a thread-like filament of cells characteristic of fungi and actinomycetes.
Immersion oil a viscous oil used to improve the resolution of a light microscope at
high power.
In vitro = ‘in glass’, i.e. outside of the living organism, in test tubes etc.
In vivo = ‘in life’, i.e. within the living organism.
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GLOSSARY 435
Inoculum the cells used to ‘seed’ a new culture.
Insertion vector a cloning vector based on phage λ that has nonessential genes
removed.
Insertional inactivation the insertion of foreign DNA within the gene sequence of a
selectable marker in order to inactivate its expression.
Interrupted mating a technique in which the order of gene transfer during
conjugation is determined by terminating transfer at different time intervals.
Intron a non-coding sequence within a gene. c.f. exon
Ion an atom or group of atoms that carries a charge due to losing or gaining one or
more electrons.
Isogamy the fusion of morphologically identical motile gametes.
Isotope forms of an element, having the same number of protons and electrons but
differing in the number of neutrons
Karyogamy the fusion of nuclei from two different cells.
Ketose a sugar molecule that contains a ketone group.
Kinetoplast a specialised structure within the mitochondria of certain flagellated
protozoans.
Koch’s postulates a set of criteria, proposed by Robert Koch, which must be satisfied
in order to link a specific organism to a specific disease.
Krebs cycle see Tricarboxylic acid cycle.
Latent period the period in a viral replication cycle between infection of the host
and release of newly synthesised viral particles.
Latent virus a virus that remains inactive in the host for long periods before being
reactivated.
Lichen a symbiotic association of a fungus (usually an ascomycete) and an alga or
cyanophyte (blue-green).
Limnetic zone a zone of a body of water away from the shore, and where light is
able to penetrate.
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436 GLOSSARY
Lipase an enzyme that digests lipids.
Lithotroph an organism that uses inorganic molecules as a source of electrons.
Littoral zone the region of a body of water situated close to land where the water is
sufficiently shallow for sunlight to penetrate to the bottom.
Lysogeny a form of bacteriophage replication in which the viral genome is
integrated into that of the host and is replicated along with it. See prophage.
Lytic cycle a process of viral replication involving the bursting of the host cell and
release of new viral particles.
Magnetosome a particle of magnetite (iron oxide) found in certain bacteria,
allowing them to orient themselves in a magnetic field.
Malting the stage in beer-making in which grain is soaked in water to initiate
germination and activate starch-digesting enzymes.
Mashing the stage in beer-making in which soluble material is released from the
grain in preparation for fermentation.
Mass number the combined total of protons and neutrons in the nucleus of an
element.
Meiosis a form of nuclear division in diploid eucaryotic cells resulting in haploid
daughter nuclei.
Merodiploid a genome that is partly haploid and partly diploid.
Mesophile an organism that grows optimally at moderate temperatures (20−45
◦
).
Messenger RNA (mRNA) a form of RNA that is synthesised as a complementary copy
of the template strand of DNA.
Methanotroph a bacterium capable of using methane as a carbon and energy
source.
Michaelis constant (K
m
) the concentration of substrate in an enzyme reaction that
results in a rate of reaction equal to one half of the maximum.
Mineralisation the breakdown of organic matter to carbon dioxide and inorganic
compounds.
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GLOSSARY 437
Minimum inhibitory concentration (MIC) the lowest concentration of an
antimicrobial substance that prevents growth of a given organism.
Mismatch repair a DNA repair system that replaces incorrectly inserted nucleotides.
Missense mutation a mutation that alters the sense of the message encoded in the
DNA, resulting in an incorrect amino acid being incorporated.
Mitochondrion a spherical to ovoid organelle found in eucaryotes. The site of ATP
generation via TCA cycle and oxidative phosphorylation.
Mitosis a form of nuclear division in eucaryotic cells, resulting in daughter nuclei
each with the same chromosome complement as the parent.
Monoecious having reproductive structures of both sexes on the same individual.
Monosaccharide the simplest from of carbohydrate molecule.
Most probable number (MPN) a statistical method of estimating microbial numbers
in a liquid sample based upon the highest dilution able to support growth.
mRNA see Messenger RNA
Mutagen a chemical or physical agent capable of inducing mutations.
Mutation any heritable alteration in a DNA sequence. It may or may not have an
effect on the phenotype.
Mutualism an association between two species from which both participants derive
benefit.
Mycelium a tangled mass of branching hyphae.
Mycorrhiza a mutualistic relationship between a fungus and a plant root.
Mycosis a disease caused by a fungus.
Neutron a subatomic particle carrying neither positive nor negative charge.
Nitrification the two-step process by which ammonia is oxidised to nitrite and then to
nitrate.
Nonsense codon see stop codon.