GLOSSARY - Introduction to the Physical and Biological Oceanography of Shelf Seas - page 377

nitrification The biological oxidation of
ammonium by bacteria to form nitrite and
nitrate.
non-linear (equation or process) Process
described by an equation involving the
products of the equation variables and
their derivatives. Non-linear equations are
usually difficult to solve analytically, so
appeal is often made to the simplifying
assumption that the non-linear terms can
be neglected and the equations thus
'linearised'.
non-photochemical quenching A mechanism
used by photosynthetic organisms to
dissipate excess energy when exposed to
high light levels and so avoiding damage to
their photosystems.
oligotrophic

use of motility in the ocean; a Pe´ clet
number >> 1 implies that swimming is a
useful trait, while << 1 indicates that
turbulent mixing overwhelms any
swimming capability.
phase speed (phase velocity) The speed of
propagation of the waves as determined for
example by observing the movement of
wave crests. The phase velocity of waves
should not to be confused with the group
velocity which is the speed at which energy
is propagated.
photic zone The region close to the sea
surface where there is sufficient light for
photosynthesis. Whether or not
photosynthesis is possible will depend on
the species within the phytoplankton
community, but typically the photic zone is
taken to reach from the sea surface to the
depth at which the surface PAR has
dropped to either 1% or 0.1% of its surface
value. Also referred to as the 'euphotic
zone'.
photoinhibition The reduction of
phytoplankton carbon fixation at high
light, due to damage of the cells'
photosystems.
photosynthetic quotient In phytoplankton,
the ratio of oxygen production during
photosynthesis to carbon fixation
(expressed as moles of oxygen per mol of
carbon).
Photosynthetically Available Radiation
(PAR) The part of the Sun's spectrum of
light that is useful for photosynthesis. It
depends on the absorption characteristics
of the phytoplankton pigments, mainly
chlorophyll a. PAR is generally taken to be
the light between wavelengths of 400 and
700 nm. A useful 'rule of thumb' is that
PAR accounts for about 50% of the total
incident radiation at the sea surface.
phytoplankton functional types Collections
of phytoplankton that have similar
functional, or biogeochemical, traits in a
phytoplankton community. For instance,
the diatoms are often treated as a single

Literally 'few nutrients'. An
oligotrophic region has one or more of the
macronutrients in negligible
concentrations. The surface layers of the
open ocean sub-tropical gyres are
oligotrophic. In shelf seas, we see
oligotrophic conditions in stratified regions
in summer.
ontogenic Relating to, or dependent on, the
age or life stage of an organism.
Ozmidov length Scale of the largest
overturning eddies in a stratified shear
flow. Kinetic energy from the mean flow is
required to increase the potential energy of
particles displaced upwards in the stratified
fluid and this sets a limit to the eddy scale
which depends on the energy dissipation
rate and the stability frequency.
PAR See Photosynthetically Available

Radiation.
particulate organic carbon (POC) Carbon

originally fixed from the pool of dissolved
inorganic carbon (DIC) by photosynthesis
and held within living organisms. POC will
not pass through a 0.45 m filter. (See also

dissolved organic carbon (DOC).)
Pe´ clet number The ratio between the
advective (e.g. swimming) and diffusive
(turbulent) components of transport. It is a
useful number when determining the likely

m