Primitive Equation Modelling ofPlankton Ecosystems
391
able in half-hour steps. They are defined by values at one-metre intervals of depth.
In addition, there is a time series ofthe exact depth (to a resolution of one millimetre) ofthe turbocline, which defines the base ofthe surface mixing layer, with continuous turbulence above, and laminar flow below. The environment contains
physical, chemical and biological variables. The physics includes temperature, turbulent kinetic energy and up- and downwelling solar irradiance in 25 wavebands.
The chemistry includes the concentrations of dissolved chemicals (nitrate, ammonium, inorganic carbon), also acidity (PH) and other chemicals required to compute
the partial pressure of carbon dioxide. The biology comprises the concentration of
plankters (number per cubic metre) of each population; also the layer-mean statistics of the biological state of those plankters, including (for phytoplankton) stored
energy and nitrogen and adaptive irradiance, and (for zooplankton) body weight,
satiation, egg mass, with derived variables. The variables in this biological environment are computed each time step from the plankton particles in the layer;
weighted by the fraction of the time that the particle spends in the layer as it
migrates through.
18.7.4 Using audit trails: a case study
Audit trails provide the modeller with a unique tool for clarifying what causes
emergent features in a Virtual Plankton Ecosystem. Each audit trail is a time series
with two parts: (1) the depth and biological state ofthe sub-population ofidentical
plankters associated with a particle, and (2) the particle's ambient environment.
A case study shows how analysing audit trails revealed the cause of a mysterious
20-day periodicity in the number of phytoplankton during summer oligotrophy,
when the pre-formed nutrients have been consumed above the nutricline (Fig.
18.3). Examination of the environment reveals that the concentration of ammonia
above the nutricline also exhibits a 20-day cycle, but in anti-phase to the phytoplankton biomass. The vertical profiles of ammonia and phytoplankton change
with this cycle (Fig. 18.3a). The cause is discovered by analysing the audit trails of
zooplankton active during the summer. After completing their diumal descent to
avoid being seen by visual predators, they feed on phytoplankton through the night
(Figs.18.3c and 18.11). The zooplankton population feeds altemately in the mixed
layer and deep chlorophyll maximum, with a 20-day periodicity. While in the
mixed layer they take ten days to graze down the phytoplankton. As they feed they
excrete ammonia, which provides a source of nitrogen to nourish future regrowth.
After reducing the phytoplankton biomass in the mixed layer to below the threshold for grazing, the zooplankton switch to feeding in the thermocline. During the
next ten days, the ungrazed phytoplankton in the mixed layer recovers, but the biomass in the thermocline is depleted. The zooplankton then switch back to feeding
in the mixed layer. So analysis of the audit trails of zooplankton revealed that they
were responsible for fertilizing surnmer growth in the mixed layer. We shall see
later (18.9) that this process contributes to the co-existence of competing populations of phytoplankton.
391
able in half-hour steps. They are defined by values at one-metre intervals of depth.
In addition, there is a time series ofthe exact depth (to a resolution of one millimetre) ofthe turbocline, which defines the base ofthe surface mixing layer, with continuous turbulence above, and laminar flow below. The environment contains
physical, chemical and biological variables. The physics includes temperature, turbulent kinetic energy and up- and downwelling solar irradiance in 25 wavebands.
The chemistry includes the concentrations of dissolved chemicals (nitrate, ammonium, inorganic carbon), also acidity (PH) and other chemicals required to compute
the partial pressure of carbon dioxide. The biology comprises the concentration of
plankters (number per cubic metre) of each population; also the layer-mean statistics of the biological state of those plankters, including (for phytoplankton) stored
energy and nitrogen and adaptive irradiance, and (for zooplankton) body weight,
satiation, egg mass, with derived variables. The variables in this biological environment are computed each time step from the plankton particles in the layer;
weighted by the fraction of the time that the particle spends in the layer as it
migrates through.
18.7.4 Using audit trails: a case study
Audit trails provide the modeller with a unique tool for clarifying what causes
emergent features in a Virtual Plankton Ecosystem. Each audit trail is a time series
with two parts: (1) the depth and biological state ofthe sub-population ofidentical
plankters associated with a particle, and (2) the particle's ambient environment.
A case study shows how analysing audit trails revealed the cause of a mysterious
20-day periodicity in the number of phytoplankton during summer oligotrophy,
when the pre-formed nutrients have been consumed above the nutricline (Fig.
18.3). Examination of the environment reveals that the concentration of ammonia
above the nutricline also exhibits a 20-day cycle, but in anti-phase to the phytoplankton biomass. The vertical profiles of ammonia and phytoplankton change
with this cycle (Fig. 18.3a). The cause is discovered by analysing the audit trails of
zooplankton active during the summer. After completing their diumal descent to
avoid being seen by visual predators, they feed on phytoplankton through the night
(Figs.18.3c and 18.11). The zooplankton population feeds altemately in the mixed
layer and deep chlorophyll maximum, with a 20-day periodicity. While in the
mixed layer they take ten days to graze down the phytoplankton. As they feed they
excrete ammonia, which provides a source of nitrogen to nourish future regrowth.
After reducing the phytoplankton biomass in the mixed layer to below the threshold for grazing, the zooplankton switch to feeding in the thermocline. During the
next ten days, the ungrazed phytoplankton in the mixed layer recovers, but the biomass in the thermocline is depleted. The zooplankton then switch back to feeding
in the mixed layer. So analysis of the audit trails of zooplankton revealed that they
were responsible for fertilizing surnmer growth in the mixed layer. We shall see
later (18.9) that this process contributes to the co-existence of competing populations of phytoplankton.