HABIT (Harmful Algal Bloom species in Thin Layers)

Thematic Priority
Global Change and Ecosystems
Project GOCE-CT-2005-003932
Harmful Algal Bloom species in Thin Layers
Publishable Final Activity Report
Contractors Involved
3.1 Instrumentation (WP2)
3.1.1 Profiler
3.1.2 Fine Scale Sampler
3.1.3 ScanFish
3.2 Cruises (WP2)
4.1 Pseudo-nitzschia
4.2 Chrysochromulina
4.3 Dinophysis
5.1 Biological processes
5.1.1 Growth
5.1.2 Nutrition
5.1.3 Vertical Migration
5.1.4 Life Cycle and Mortality
5.2 Small Scale Physical processes
5.2.1 Shear (S) Shear and the case of a thin layer of Chrysochromulina sp.,
Bay of Biscay, 2006 Shear and the case of a thin layer of Pseudo-nitzschia, Ria
de Pontevedra, 2005
5.3 Scale and Niche of Dinophysis communities
6.1 Model Approaches
6.1.1. Bay of Biscay Model (MARS 3D)
6.1.2 The Celtic Sea Model
6.2 Model Outputs
6.3.1 Dinophysis blooms in the Bay of Biscay.
6.3.2 Dinophysis blooms in South-western Ireland.
6.3 Conclusions
10.1 Origin of Dinophysis blooms
10.2 Offshore Observatories
10.3 Incorporation of models into monitoring regimes
1. Summary Description of Project Objectives
The project HABIT researched the development and dispersion of HAB populations in sub-surface
micro-layers. It focused on the genus of phytoplankton, Dinophysis, that has the most serious
impact on the economic development of the European coastal zone through contamination of filter
feeding shellfish with Diarrhoeic Shellfish Poisons (DSP). Populations of this genus frequently occur
in sub-surface, thin micro-layers.
The overall objective of HABIT was therefore to resolve
fundamental patterns in the occurrences of Dinophysis and quantify the processes that are
important in governing their distribution. To this end, the approach of the project HABIT was
To investigate the maintenance and persistence of high density thin layers through
studying interactions between fine scale physical diffusion and net growth and trophic
relationships within them
To investigate the precise role of small scale structures on the coastal shelf as incubators
for accumulations of Dinophysis
Utilise physical models to examine the formation and persistence of gyres and other
small scale structures on the shelf, to predict their transport, and as a consequence HAB
events at the coast.
Contractors Involved
Co-ordinator : National University of Ireland, Galway
Dr. Robin Raine
The Martin Ryan Institute
National University of Ireland, Galway,
Partner: IFREMER
Dr. Patrick Gentien,
Pointe du Diable,
B.P. 70, 29280 Plouzane,
Partner: Instituto Español de Oceanografía
Dr. Beatriz Reguera
Instituto Español de Oceanografía
Centro Oceanográfico de Vigo
Cabo Estai - Canido. 36200 Vigo,
Partner: CEFAS
Dr. Liam Fernand,
Pakefield Road,
Suffolk NR33 0HT
United Kingdom
Associated US project co-ordinator:
John Hopkins University
3400 North Charles Street
MD 212182695, USA
2 Approach Used and Significant Findings
The negative impact of harmful algal blooms can only be prevented through resolving fundamental
patterns in their occurrences and quantifying the processes that are important in governing their
distribution. To this end, the project HABIT from the outset was to focus on the harmful genus
Dinophysis through:
an investigation of the maintenance and persistence of high density thin layers of Dinophysis
through studying interactions between fine scale physical diffusion and net growth and
trophic relationships within these layers
investigating the precise role of small scale structures on the coastal shelf (small gyres,
pycnoclines) as incubators for accumulations of Dinophysis spp.
utilising physical models to examine the formation and persistence of gyres on the shelf, to
predict their transport, and as a consequence, HAB events at the coast.
The accumulation of information regarding the occurrence of HAB species in thin layers has been
slow and sporadic. This is mainly because the sub-surface layer can be present at any depth in the
water column, but also because measuring instruments now considered as standard (such as in situ
fluorometers) are not always able to observe them, and hence cannot target them for sampling.
The net result is that this indicative information is poorly disseminated and not available through the
normal channels such as the scientific literature.
Very little is known about the nutrition, behaviour and trophic relationships within thin layers of
phytoplankton. HABIT dealt with this challenging task by measuring organic compounds in fractions
based on molecular weight and investigating their relative influence on growth. This was the first
attempt to study this aspect for Dinophysis, a genus for which information is non-existent due to a
historical inability to culture this organism. Several further questions are addressed: are the
Dinophysis cells always imbedded within optically detectable layers using spectral optics techniques?
Are they associated with layers of dissolved organic matter? Are they usually in the steepest part of
the pycnocline? Do they vertically migrate, or change vertical position by swimming behaviour?
The physical processes relevant to thin layers occur at many length scales. Many of the longer scale
processes such as tides, meteorological forcing (solar input, wind etc), inertial waves, and sub tidal
internal waves are routinely observed with standard instruments and are well modelled through 3-D
baroclinic models and meteorological models.
Recent advances in technology (principally
microelectronics) have led to affordable high frequency instrumentation suitable for measuring
physical processes at smaller scales. Achievement of a profile of the microstructure of turbulence
can be constructed using free-fall probes (Burchard et al., 2002), via techniques using ADCPs to
measure shear stress (Rippeth et al., 2002), or via high frequency 3 axis current meters. Estimates
of horizontal mixing are more difficult to measure and are best obtained by the use of tracers.
It is recognised that thin layers of dinoflagellates (and other HAB taxa) can require retention zones or
other small-scale structures on the coastal shelf for populations to develop with a high-density.
These zones were investigated as incubators for, and transporters of, thin layers of Dinophysis. 3D
physical models were utilised at a high enough resolution such that the persistence and movement
of these structures can be modelled.
In this way, HAB dynamics were shown to depend on the
hydrodynamic regime of the coastal ocean.
Significant findings beyond state of the art
The most significant findings of the work output from HABIT can be summarised as follows
High density sub-surface layers of a variety of potentially harmful species exist. These can
be extremely difficult to sample using conventional sampling methodologies
The scale of populations of Dinophysis, which can be considered a rare species, is very small,
occurring in thin layers (0.5-5m thickness) in patch size of less than 10 km x 10 km
Sub-surface layers of Dinophysis arise offshore but do not always impact on the coast.
The mixotrophic nutrition of Dinophysis is complex, and in the case of particulate nutrition
seems to be highly opportunistic.
The processes involved in transporting these populations can now be modelled using high
quality (and resolution) 3D physical models.
There follows a scientific summary of tasks carried out and results achieved.
3. Methodologies
In addition to the traditional shipboard sampling techniques (e.g. CTD rosette samplers), three key
equipments were used during the programme for studying thin layers: the IFREMER Profiler, the
Fine-Scale Sampler, and Scanfish. These are outlined in more detail below. High vertical resolution
measurements of shear were made using high frequency ADCP.
3.1.1 Profiler
The IFREMER high resolution particle size profiler (Fig. 3.1) was the instrument most often deployed,
fitted with a peristaltic pump (Fig3.1) so that large volume water samples could be achieved from a
targeted depth. In addition to the in situ particle size analyser and CTD, the package contained
fluorometers, turbidity sensor, a video microscope and latterly a fluoro-microscope.
Figure 3.1 (above). The IFREMER particle size profiler
Figure 3.2 (Right). The IFREMER Fine Scale Sampler
3.1.2 Fine Scale Sampler
The IFREMER Fine Scale sampler (FSS) takes a simultaneously takes a suite of 15 water samples
which are 20 cm apart (Fig. 3.2). The sampling bottles are arranged horizontally and triggered
electronically. The FSS was deployed at selected stations on most field exercises.
3.1.3 ScanFish
The Scan Fish (Figure 3.3) is a towed undulating CTD, with additional sensors for irradiance (PAR),
fluorescence and turbidity. Its advantage lies in the resolution attainable in the vertical whilst
towed at relatively high speed (8-10 knots). Subject to ship’s speed and water depth, a vertical
profile can be achieved every 400 m.
Figure 3.3. ScanFish
3.2 Cruises (WP2)
Research expeditions were carried out in three areas of the Atlantic seaboard of Europe. These
were the Galician Rias of northwestern Spain, the Bay of Biscay and the continetal shelf region off
southern Ireland. The meta data comprising the location of stations sampled, date and time, and
what instrumentation was deployed at each station can be found in the detailed cruise reports
supplied for each cruise. The surveyed areas and sampling locations are summarised in Figures 3.43.6.
Figure 3.4. Station Sampling positions, Ria de Pontevedra, June 2005.
Figure 3.5. Station sampling positions, Thalassa HABIT cruise, Bay of Biscay, July 2006
Figure 3.6. Station sampling positions, Celtic Explorer HABIT cruise, southwest Ireland, July 2007.
4. Thin Layers
Thin layers of phytoplankton were observed on all collaborative field exercises. High density (>5000
cells l-1) thin layers of Dinophysis were not observed until the cruise off the south coast of Ireland in
2007. Detailed summaries of the phytoplankton composition can be found in D07 and in the data
files currently located at the project ftp site (www.toxicblooms.com).
4.1 Pseudo-nitzschia
Thin layers of Pseudo-nitzschia were present in both Galician ria cruises in 2005 and 2007 and in the
survey off the south coast of Ireland, also in 2007. Velo-Suarez et al. (2008) describe the behaviour
of the thin layer of Pseudo-nitzschia during an upwelling-downwelling cycle in the Ria de Pontevedra
observed during the collaborative field exercise in 2005.
Figure 4.1
A thin layer of chlorophyll fluorescence, Ria de Pontevedra, station HV05159. The
fluorescence maxima comprised a bloom of Pseudo-nitzschia.
4.2 Chrysochromulina
A thin layer of Chrysochromulina sp. nov. was observed in the eastern (coastal) Bay of Biscay in
2006. High cell densities (2-8 x 106 cells l-1) were observed at density discontinuities in this region,
an observation confirmed through the deployment of the Fine Scale Sampler (Fig. 4.2).
Measurements of shear were carried out in the vicinity of this layer (see section 6.2).
Figure 4.2. A thin layer of Chrsochromulina sp. sampled off the south coast of Brittany, July 2007.
4.3 Dinophysis
High density thin layers of Dinophysis acuta were observed off the south coast of Ireland in July
2007. Cell densities achieved up to 55000 cells l-1. The layer was present as a patch of order 3 Km
in diameter and thickness 3 metres. A bloom of Pseudo-nitzschia was occurring at the time. A
secondary high density thin layer was also observed comprising equal numbers of D. acuminata and
D. ovum. This layer was <40 cm thick, more local (smaller patch size) than the D. acuta layer and
observed within the D. acuta layer.
Figure 4.3
A high density thin layer of Dinophysis acuta sampled off the south coast of Ireland,
July 2007.
Figure 4.4.
Section of a thin layer of Dinophysis acuta sampled between 17.5 and 20.5 m depth.
Note that within the layer is a secondary thin layer comprising high densities of
Dinophysis acuminata and Dinophysis ovum. (SW Ireland, station 70, July 2007).
5. Maintenance of Thin Layers
A number of in situ and laboratory experiments were carried out in an effort to determine the
relative importance of the balance between physical and biological processes in maintaining thin
layers of Dinophysis. Relevant biological processes included growth, migration, nutrition and
mortality whereas substantial effort was made to look at the effects of shear in controlling thin layer
5.1 Biological processes
5.1.1 Growth
In general, maximum values of µ, the in situ division rate, several times higher than the background
or average µ, were found in the Galician Rías co-occurring with the cell maxima (Figure 5.1.1. See
also Velo-Suárez et al., accepted). In these cases, we could describe “thin layers of µ”.
In the Bay of Biscay in July 2006, moderate values of µ (0.23 d-1) were estimated in a population that
exhibited its maxima just above a steep thermocline, with a high cell viability (89%), but the
population still declined a few days later (Velo-Suárez et al., 2008b).
Model output results show
that the decline in the population was due physical export.
Vertical profiles of µz estimates (dashed lines) and cell counts (solid lines) for
(A) Dinophysis caudata and (B) Dinophysis acuta in the Ría de Vigo (stn. V5, August).
Figure 5.1.1.
Nevertheless, in SW Ireland in July 2007, estimates of µmin (approx. 0.1 d-1) were constant
throughout a 2-3m high density thin layer of D. acuta, and at depths away from the layer. This is
potentially significant as it suggests that the high cell densities observed in the layer resulted from
transport or other physical means as opposed to high division rates. In this cruise, a high frequency
of viable cells (80-100%) was observed both within the thin layers, and in the layers above and
below. At some stations however, there were important vertical differences in this parameter with
lower viability at lower depths, which may suggest the existence of sinking areas.
The conclusion is that range of vertical and diel heterogeneity in the growth rate demands specific
experimentation to attain accurate values of growth.
5.1.2 Nutrition
Dinophysis At the start of the project Dinophysis was known to be mixotrophic.
At the outset,
experiments with Dinophysis were planned to see how well the organism could live on fractions of
dissolved organic material DOM) in varying size (molecular weight) classes, or fractions.
experiments were carried out in the Galician Rias in 2005 and in the Bay of Biscay in 2006. Fractions
of DOM were prepared by ultracentrifugation.
From all of these results it can be expected that Dinophysis spp. exhibit a high plasticity in their
particulate feeding behaviour. This may show an alternance of periods of replenishment (high
frequency of vacuolation) with periods of Mesodinium-starvation. Dissolved organic matter, small
dinoflagellates and maybe even other unknown organic sources may assist in the survival of
Dinophysis populations in suboptimal conditions in times of Mesodinium-limitation.
From all of the observations, we propose for Dinophysis a highly opportunistic feeding strategy. The
organism acquires a huge amount of food (that deforms its contour) when they bump into their
optimum prey (Mesodinium) and surviving in suboptimal conditions (DOM, others) in between.
These ideas were presented in an oral communication (Reguera et al., 2008) at the 13th International
Conference on Harmful Algae (13th ICHA) (Hong Kong, 3-7 November 2008).
5.1.3 Vertical Migration
Previous studies with D. acuminata (Reguera et al. 2003) and D. acuta (MacKenzie 1992) have shown
evidence of diurnal vertical displacements in Dinophysis populations. However, there have also
been a substantial number of instances where Dinophysis spp. have appeared to remain in a specific
water layer and show no migration patterns (reviewed in Maestrini, 1998). Furthermore, in the Ria
de Vigo, Villarino et al. (1995) have reported that D. acuminata and (its ciliate prey) Mesodinium
rubrum exhibited a common daily vertical migration, between 7 m and the sea surface.
During the HABIT-Vigo 2005 cruise, a 24-h sampling was carried out to re-address the question of
whether Dinophysis poplations migrate in the Ria de Pontevedra (González-Gil et al. in prep.).
Figure 5.1.5 shows key results of this survey. In contrast with M. rubrum, D. acuminata did not
show a clear migration pattern and remained in the warmer surface layer. Throughout the whole
HABIT-Vigo 2005, Dinophysis cells appeared constrained in this layer, and the cell maxima were
associated with the diurnal thermocline (Velo-Suárez et al., 2008a).
Figure 5.1.5
Vertical distribution of Dinophysis acuminata (open circles) and Mesodinium rubrum
(filled circles) during a 24-h sampling at station P2 in Ría de Pontevedra (13-14 June
During a second 24-h sampling of D. acuta in the autumn, vertical migration was again not observed,
and the cell maxima appeared around a near surface halocline (Pizarro et al., 2008). It was
concluded that different species of Dinophysis, or even the same species in different locations, or
even in different seasons in the same location, may exhibit different migratory patterns. Therefore,
the same species may switch from a population that migrates to one with a layer-forming behaviour.
In all cases, , Dinophysis spp aggregate as if they had a social behaviour, whether there is a clear
migratory vertical displacement or not. This appears to be preferentially around a physical cue such
as pycnoclines, haloclines, the diurnal thermocline, (or other clines) that does not necessarily
coincide with the layer of maximum density-discontinuity. Its behaviour is most likely determined
by its nutritional status (replenished or starved) and by different phases in the population growth.
Some intriguing questions remain with respect to Dinophysis migration:
How can Dinophysis chase its fast-swimming prey, M. rubrum ?
Is Dinophysis attracted towards its prey by some chemical substances?
The results of Villarino et al. (1995) would tend to suggest that the migratory pattern of Dinophysis
mimicked that of Mesodinium. Nevertheless, recent HABIT observations (González-Gil et al.. in
prep; Figure 5.1.4) suggest that rather than Dinophysis chasing Mesodinium, the latter collides with
Dinophysis during its own migratory route and its trapped by the dinoflagellate by means of some
still unknown mechanism.
5.1.4 Life Cycle and Mortality
Dinophysis populations exhibit a high plasticity in their life cycle transitions. This explains their
persistence in the water column: planozygotes can divide directly with no need to mature into
resting cysts and go through mandatory dormancy periods (Escalera and Reguera, 2008), a process
which makes studies on other organism such as Alexandrium more straightforward.
Cell mortality was indirectly measured by estimating the frequency of empty theca of Dinophysis.
Results hve been analysed in tandem with the frequency of viable cells, identified after staining with
fluorescein diacetate (FDA) (Gentien, 1986) and in vivo observation at the epifluorescence
microscope. High frequencies of viable cells were observed at all locations. For example in the
Galician Rias, values were of the order 80-90%, although occasionally dipping to 50-60% through a
cycle in the Ria de Pontevedra in 2007 (Fig. 5.1. 3). High cell viabilities were also observed in the
Bay of Biscay in 2006 (85-90%) and of the south coast of Ireland in 2007 (80-100%). Parasitism,
although present (max. about 2%), did not seem to constitute an important factor in the population
dynamics (decline) of D. acuminata .
5.2 Small Scale Physical processes
Maintenance of thin layers results in the balance between physical and biological processes acting
on and within them. Within the stratified environment, of key relevance in the context of thin
layers is the Richardson number Ri. The Richardson number is the ratio between the buoyancy
force, i.e. degree of stratification, which stabilises a system, to the current shear, which will act
towards making a system more turbulent. The degree of stratification is calculated from the Brunt
Vaisala frequency, N, whereas the shear (S) is calculated (stepwise) from the gradient in currents.
The equations used are :
Ri 2 
g  
N 2  
  z 
du 2 dv 2
S 2      
dz  dz 
where g is the acceleration due to gravity, r the water density, and u and v the east and north
components of the current at depth z.
It is generally a necessary condition for shear flow instability to occur that Ri is <0.25 somewhere in
the flow, or for a stable system for Ri > 0.25 everywhere. Away from the surface and bottom
boundaries shear is greatest in the thermocline and it is this area that is most likely to experience
turbulence from shear.
5.2.1 Shear (S)
Whereas the Brunt Vaisala frequency is relatively easily achieved from CTD data, the vertical profile
of horizontal shear is less easily obtained at a high enough vertical resolution. To this effect, high
frequency ADCP current meters were used to obtain the shear profiles. The data set for offshore
studies with the highest resolution was obtained during the Thalassa 2006 Bay of Biscay survey.
Here, current profiles were obtained using a RDI Workhorse ADCP was suspended at a selected
depth on the CTD frame for a suitable time period (5-10 minutes). To obtain the shear profile,
profiles of the north and east component of the currents were smoothed, and shear profiles were
obtained from the output. A worked example is shown in Figure 5.2.1.
Figure 5.2.1
Attaining shear profiles from current data. Data are from station HB68 in the Bay of
Biscay, July 2006. Smoothing was carried out using non-linear regression with 5th
order polynomial. Shear and the case of a thin layer of Chrysochromulina sp., Bay of Biscay, 2006
During the Biscay survey in 2006, a high density thin layer of Chrysochromulina sp. nov. was
observed. Figures 5.2.2-5.2.5 give examples of profiles taken from stations sampled near the coast,
away from the coast and further offshore. Inshore (Fig. 5.2.2), the bloom has developed in the
bottom mixed layer of a shallow water column, where very high densities have resulted from
exploitation of the nutrient and light rich environment. As one moves further offshore, the bloom
has spread along its isopycnal. At these offshore stations, the fluorescence maxima, entirely due to
the Chrysochromulina population, coincided with the region of maximum Richardson number,
indicating a passive spreading of the population away from the coast along the isopycnal (with value
of 26.6). The position of the chlorophyll maximum was close to the position of maximum shear, but
the problem of internal waves meant that this could not be observed with certainty.
Figure 5.2.2
Profiles of density with Brunt-Vaisala frequency, shear, Richardson number,
chlorophyll fluorescence and Chrysochromulina sp. at station 68, close to the coast.
Figure 5.2.3
Profiles of density with Brunt-Vaisala frequency, shear, Richardson number,
chlorophyll fluorescence and Chrysochromulina sp. at station 60, a 10 km away from
the coast.
Figure 5.2.4
Profiles of density with Brunt-Vaisala frequency, shear, Richardson number,
chlorophyll fluorescence and Chrysochromulina sp. at station 71, ca 25 km away
from the coast.
These observations have been summarised by Farrell et al. (submitted). However, an overall
impression of the extent of the bloom can be achieved through a ScanFish section running normal to
the cost through the bloom (Figure 5.2.5).
Figure 5.2.5
ScanFish section showing distribution of chlorophyll fluorescence along transect 72
(for location see inset map), southern Brittany, July 2006. The Chrysochromulina
bloom is the region of high fuoescence between km 67 and km 90.
16 Shear and the case of a thin layer of Pseudo-nitzschia, Ria de Pontevedra, 2005
On 02 June 2005, CTD profiles in the Ria de Pontevedra revealed a subsurface Chl a maximum (SCM)
located between the 26.9 and 27.1 isopycnals (Figs. 5.2.6, 5.2.7). A day later, Chl a values increased
and its maximum persisted associated with the maximum density gradient in the pycnocline. The
SCM was located slightly below the depth where N2 was maximum (> 2.5x 10-4 (radians s-1)2). High
shear values below the pycnocline resulted in high values of  and low values of Ri, i.e. decreased
stability below the SCM at the bottom of the pycnocline (Figs. 5.2.6, 5.2.7).
On 06 June, the SCM became thinner (< 5 m) and profiles from other sampling stations confirmed
the horizontal extension of the layer in the whole Ría (Velo-Suárez et al. 2008). The upwelling event
occurring at the time promoted the inflow of the Atlantic water at the bottom and the elevation of
the TL located at the pycnocline that became more pronounced. However, on 08 June,a relaxation of
northerly winds promoted the vertical displacement of the layer from 6-10 m to 9-13 m. The TL
location during this period was at the layer of maximum N, and the water column remained
significantly more stratified and stable (high Ri). Nevertheless, lower values of Ri were associated
with increased shear and mixing at the base of the layer. The TL was associated with the maximum
shear in the water column and its thickness determined by that of the maximum shear region (0.025 to 0.025 s-1). Minimum values of turbulence were found below the 27.1 isopycnal during the
upwelling pulses (below 10-9 m2 s-3).
Downwelling favourable winds after 08 June resulted in the thickening of the TL from 4 m to 10.5 m
thickness, and its final dispersion and displacement to the bottom at the end of the survey. These
events coincided with the weakening and disappearance of the stepped structure in the pycnocline
and the lowest values of N2 found during the survey. Increased levels of shear and low values of Ri
(high instability) at the bottom where the SCM was being displaced, could be observed. High
turbulence dissipation rates in the bottom layers also increased when downwelling started (Fig
On 13 June, a new strong density discontinuity at 10 m depth appeared due to the intrusion of the
downwelled waters (16ºC). However, a secondary N2 maximum (density 27.1) could also be
observed at 25 m where the TL was originally located.
The thickness of the observed Chl a structure during this survey was related to the velocity field that
promoted different shear profiles. During the initial and final periods, the SCM was located within or
adjacent to a change in the direction of horizontal velocity in a layer of no-motion (between inflow
and outflow waters). On the other hand, between 6-8 July the whole water column was found to
move in the same direction (inflow). However, vertical heterogeneities in the horizontal velocity
promoted the formation of a high and thin shear region where the SCM was located. Changes in the
shear profile resulted in changes in the Chl a peak intensity and thickness from medium broad, to
thinner, then broad and finally dispersed (Fig 5.2.6; 5.2.7).
Figure 5.2.6
Vertical distribution, from 02 to 13 June 2005, of (a) water current velocity (m s-1),
(b) shear (s-1) and (a) seawater density (27 and 27.1 σt isopycnals) and (b-c) Chl a
concentration (μg Chl a L-1) as contour lines.
Figure 5.2.7
Vertical distribution of Chl a concentration (μg Chl a L-1) (A-date panels), buoyancy
frequency (N2; (radians s-1)2) (B-date panels), Richardson number (Ri; log scale) (Cdate panels), and shear squared (s-1) (D-date panels) at station 2 in the Navigation
Channel of the Ría of Pontevedra from 02 - 03 June (Case 1) 2005. Depth range of
the Chl a structure found is shaded.
Physical processes governed the formation, maintenance and dissipation of a thin layer during a
two-week survey in the Ría de Pontevedra. The SCM was always associated with the depth of
maximum shear and differences in shear profiles led to the formation of a thin layer during the
upwelling event. The effect of shear upon phytoplankton patches, which have been predicted on the
basis of theoretical studies, has been corroborated in this study. Although the TL was associated
with maximum vertical shear, high values of N2 indicated that this region was sufficiently stable to
suppress turbulent vertical mixing that would have dissipated it.
The strong relationship found between thin layers and physical structure indicates that it is not
possible to understand the spatial and temporal occurrence of these layers without understanding
both local circulation patterns and regional physical forcing.
5.3 Scale and Niche of Dinophysis communities
In July 2007 sampling off the south coast of Ireland was carried out using the IFREMER in situ particle
size analysis profiling system.
Observations at one of the initial stations revealed a high density
layer of D. acuta lying close to, but not within, the chlorophyll maximum at the base of the surface
mixed layer (Fig. 5.3.1). the population had a dimension of order 3 km in the direction of the tidal
stream, which flowed parallel to the coastline. This deduction was based on the disappearance with
time of the population after repetitive sampling with the vessel platform in a geostationary position.
Sampling transects normal to the coastline demonstrated that the populaton was present as a patch,
with cross section of similar magnitude. Thus the geographic niche the population was occupying
was close to 9 Km2 by 3 m thick. The cell density within the layer (20,000-55,000 l-1) was sufficiently
high to create serious problems of shellfish toxicity. This is the first direct evidence of the scale that
hydrodynamic models need to accomodate to successfully predict harmful events.
The patch was located within the coastal jet current which is a baroclinically driven flow, parallel to
the coast, caused by the increasing contribution of tidal mixing to stratification as the water column
shallows. The patch was followed over a period of seven days drifting westwards at a (residual)
speed of 6.5 Km d-1, the same as that previously measured for the coastal jet in this region.
Application of a high resolution 3D physical model, using a passive (neutrally bouyant) tracer,
mimicked observations extremely well (see Section 5.3). The ultimate origin of the population still
remains obscure, even though its position suggested that it had come from a location on the
continental shelf.
6. Modelling
6.1 Model Approaches
High quality physical models have been employed to simulate movement of small scale physical
structures which can act as incubators or transport thin layers of Dinophysis. Physical modelling in
relation to blooms of Dinophysis were confined to Biscay and the Celtic Sea for operational regions.
Summaries of hydrographic processes occurring in both areas can be found in Brown et al (2000) and
Lazure et al (2008) (D21).
6.1.1. Bay of Biscay Model (MARS 3D)
The Bay of Biscay (MARS 3D) model extends from 8°W to the French Atlantic coast and from the
Spanish coast to 50°30’N thus encompassing the entrance of the English Channel. The eastern
boundary in the Channel is set at 3°W. The horizontal resolution is of 4 km, 30 vertical levels are
considered and refined near the surface. The kernel of the MARS3D model has been fully described
by Lazure and Dumas (2007). It is a mode splitting model with an original coupling of the barotropicbaroclinic modes within a sigma coordinates framework. The application to the Bay of Biscay has
shown that the tide is accurately simulated and the comparison with currents profiles records are in
acceptable agreement for short time range.
6.1.2 The Celtic Sea Model
In the original HABIT proposal the in house modelling system was the Princeton Ocean model. After
the proposal was written the need to develop ecosystem modelling capability became evident which
ultimately led to the requirement of a power computer cluster, and the associated requirement to
run modelling codes that worked on parallel machines. The choice made by CEFAS was to move to
the 3D General Estuarine Transport Model (GETM) public domain model.
6.2 Model Outputs
6.2.1 Dinophysis blooms in the Bay of Biscay.
Dinophysis events along an open coastal system like the Bay de Vilaine, southern Brittany, result
from the following succession of events:
1. Accumulation and growth of a toxic population in a gyre
2. Retention within the gyre occurs for a period sufficient to allow a build-up of the population
3. Advection to the coastline where shellfish may be contaminated.
It was not possible to test this retention hypothesis during the HABIT cruise on board the R/V
Thalassa in 2006 due to observations of only a weak population of Dinophysis. However, the
success of applying the MARS 3D model in predicting the occurrence and movement of gyres that
encroach on the Bay de Vilaine in Brittany is the topic of HABIT publication 2 (Xie et al, 2007). Here
the model was applied in hindcast and clearly shows the movement of gyres into the area of concern
the Bay de Vilaine, (BV) (Fig. 6.2.1).
Figure 6.2.1 Model outputs showing the residual current field and the movement of gyres towards
the Bay de Vilaine, southern Brittany on a) March, 29th 1996, (b) April, 1st 1996, (c)
April, 4th 1996, (d) May, 10th 1998, (e), May, 14th 1998 and (f), May, 17th 1998 (f).
Vectors of currents are drawn for every fourth grid node.
6.2.2 Dinophysis blooms in South-western Ireland.
The key area of interest in terms of shellfish aquaculture production and harmful algal events is
Bantry Bay and the adjacent bays of Dunmanus and Long Island which give south-western Ireland its
characteristic appearance in the coastline. Harmful blooms arise through the alongshore transport
of potentially harmful populations in the coastal baroclinic jet-like flows which run around the
coastal perimeter of the Celtic Sea. When at the mouths of these bays, fluctuations in wind cause
two layer oscillatory flows that exchange water in the bays with that on the near coastal shelf. The
prerequisite here is a stratified water column for both these mechanisms to occur.
In July 2007 the direct observations of transport of a high density Dinophysis population in a thin
layer within a coastal jet resulted from the HABIT field exercise planned for the region. These are
the first direct observations of transport of HABs within coastal jets. The GETM model was run in
particle tracking mode, with an initial input of particles at the depth and location of the first
observation of Dinophysis in a thin layer. A comparison of model output with field observation is
shown in Figures 6.2.2 -6.2.4. Very close agreement between model output and field observations
were achieved.
Figure 6.2.2
GETM model results using the initial observed location of a high density Dinophysis
population at 17 – 19m depth. Times 1, 2, 3 and 4 (left to right) are July 23rd 0800, 25th
0800, 27th 0800 and 29 th 0800, respectively. Top Row: wind only, no density effects.
Middle Row: simulated density effects only no wind. Bottom Row: wind and
simulated density effects combined.
Figure 6.2.3 . Predicted positions (red circles) from model output of Dinophysis acuta population in
the northern Celtic Sea. The end position observed is placed for reference.
D. acuta > 5,000 c ells/l
Latitude (N)
51 42’
Sampling stations
51 18’
Longitude (W)
Figure 6.2.4. The progression of the location of observed Dinophysis acuta population over the
period 23-29 July 2007.
Compare the continuous westward movement of the
population with that predicted in Figure 6.2.3.
6.3. Conclusions
Physical models are now available which have a satisfactory resolution that incorporates,
realistically, the small scale features such as gyres and coastal jets that are important in the
transport of populations of harmful algae onto the coastline. Importantly, even if these are present
as sub-surface thin layers, the populations can still be incorporated into the models.
7. Prediction of DSP Events
Prediction of harmful events, including DSP events derived from the presence of Dinophysis, requires
an implementation of the models described above in operational mode. Unfortunately, this was not
possible during the lifetime of HABIT. However, it was possible to use the approach used for the
Bay of Biscay in hind cast mode.
For the southwest of Ireland, there is not enough historical data to do such a hind cast with the
model approach used. Instead, during HABIT, the implementation of a bloom prediction logic
model based on the weather forecast was applied. This is due to the advection of HABs into the
bays where shellfish culture is carried out is wind forced (see HABIT submission Raine et al, 2008). If
the wind changes are correct and the time of year correct, then there is a high probability of a
harmful bloom. The idea was developed and put into operational mode. The key result is in Figure
6.1, which shows the likelihood of an exchange event (the wind index) based on the weather
forecast, based on real data, in connection with the timing of a harmful DSP event in 2005.
Figure 7.1
Predicting harmful algal events in Bantry Bay, southwestern Ireland. The wind index
obtained from 5-day weather forecast is plotted against actual values measured at both
Valentia and the M3 Weather Buoy (see Figure 1 for respective locations). Exchange
events are predicted for 18 May, 16 and 30 June, and 16 and 30 July. On each
occasion, water exchange as sown in the bottom temperature record took place. The
event of 16 June was followed by an increase in cell densities of D. acuminata and
shellfish harvest closures were in operation in Bantry Bay from this date.
8. Added Value
From a scientific viewpoint, a significant added value of the programme has been the discovery of
two new species, one of Fragilidium (F. duplocampanaeforme, Nezan�and Chomerat, 2008) and an
as yet undesignated species of Chrysochromulina (see Farrell et al, submitted). Furthermore,
cultures of a second suspected new species of Fragilidium have been isolated from the 2007
Explorer cruise off the south coast of Ireland.
Another finding that occurred during the course of the HABIT studies was the observation of
digestive vacuoles full of phycoerithrin-like pigments in the obligate heterotroph Dinophysis
rotundata and in its co-occurring ciliate prey Tiarina cf fusus. This, along with toxin analyses of
single cell isolates of D. rotundata and other accompanying species of Dinophysis spp., has led us to
propose that D. rotundata does not produce toxins de novo, but rather acts as a secondary vector of
DSP toxins, produced by co-occuring phototrophic species of Dinophysis, that are eaten by its ciliate
prey. These results were presented in a poster at the 13th ICHA (González-Gil et al., 2008) and are
included in a document under preparation.
9. Recommendations for Future Work
9.1 Origin of Dinophysis blooms
The precise origins of the Dinophysis blooms in the three regions of concern of HABIT remain elusive.
This has mainly arisen from the absence of established blooms in the Bay of Biscay and in Galicia
during co-operative field exercises, and due to the motile nature of the established thin layer bloom
off the south coast of Ireland. There were however clues to the origin of the Irish bloom in that
viable populations of reasonable density (2000-3000 cells l-1) close to the seabed (Farrell et al, 2009;
Fux et al, 2008). This is not, in the global sense, the first time populations have been observed in this
environment and their association with the benthic boundary layer should be investigated as a
possible origin.
9.2 Offshore Observatories
It is clear that Dinophysis blooms are transported physically into sites used for shellfish aquaculture.
In some cases, the transport system is weather driven and as a consequence blooms may be
predicted using weather forecast and time of year approach as in Raine et al (2008). The range of
this prediction is however linked to that of the weather forecast, i.e. a maximum of only five days.
Species of Dinophysis are relatively large (50-70 microns in length) and most, if not all that are found
along Europe west coast are toxic.
It should therefore be possible to establish offshore
observatories that are capable, in real time, of sending back information on the presence of
Dinophysis, therefore increasing considerably the forecast range. Given the size of Dinophysis, these
observatories could be optically based, as opposed to the rather complex ones currently being
trialled based on molecular biology reactions such as the Environmental Sample Processor (ESP)
methodology (Greenfield et al., 2006).
9.3 Incorporation of models into monitoring regimes
A significant outcome of the HABIT project has been the ability of high resolution 3D models to
reproduce the transport of Dinophysis populations in thin layers. Given their accuracy, and the
current rate of incorporation of computing power into smaller and more manageable units, and thus
easier and more user friendly to operate, the feasibility of transferring the models into management
systems operated by key stakeholders such as monitoring agencies and hence providing industry
with valuable data on prediction
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