Presentation by Lisa Schneider (Deltares, Netherlands), at the Delft3D User Days, during Delft Software Days - Edition 2022. Tuesday, 15 November 2022.

1. Lisa K. Schneider, Lora Buckman, Nathalie Gypens, Michelle Jeuken, Maarten Klapwijk,
Arjen Markus, Tineke A. Troost, Lauriane Vilmin, Luca van Duren, Willem Stolte
Modelling phytoplankton, mixoplankton &
protozooplankton
PROTIST - a new primary
production module for
D-Water Quality

2. introduction
:
PROTIST
:
application
:
conclusion
Primary producers such as (phyto)plankton form the base
of marine coastal ecosystems.
2
Eutrophication
Carry capacity
Harmful Algae
Blooms
Carbon fluxes
Numerical Model
Hydrodynamics + Sediment Dynamics + Water Quality + …

3. introduction
:
PROTIST
:
application
:
conclusion
DELWAQ is the water quality component of the Deltares
numerical modelling suite.
3
plankton
DYNAMO BLOOM
Two different modules
to simulate plankton
and primary
production

4. introduction
:
PROTIST
:
application
:
conclusion
These two primary production modules differ in their
mathematical principles applied.
4
DYNAMO BLOOM
Monod kinetics Linear programming
Small time step
→ Turbulent
systems
Species competition
Simple
→ Too simple
24 h time step
→ Difficult in
turbulent
systems
→ Difficult in
species
ecosystem
interaction

5. introduction
:
PROTIST
:
application
:
conclusion
Hot topic in coastal zone management is the combination
of offshore wind farms with different forms of aquaculture.
5
+
Integrated multi-trophic
aquaculture (IMTA)
Primary production module requirements: Small time step
→ Interspecies competition
→ Turbulent systems
Multiple species
Offshore wind farms
Planktonic primary production
+

6. introduction
:
PROTIST
:
application
:
conclusion
DELWAQ recently released a new primary production
module called PROTIST.
6
plankton
DYNAMO BLOOM PROTIST
Three different modules
to simulate plankton and
primary production

7. introduction
:
PROTIST
:
application
:
conclusion
7
PROTIST is a primary production module for DELWAQ
that models the complete protist community.
PROTIST
5 protist functional types simultaneously
Schneider et al.
(2021) Modelling
mixoplankton along
the biogeochemical
gradient of the
Southern North Sea.
Ecological Modelling,
459.
ligh
t
NO3
- NH4
+
CO2,NH4
+,DIP
DIP
DO
M
PO
M
CO2
pre
y
SAPPM
1 protist functional type at a time
Flynn (2021) Enhancing Microalgal Production
- constructing decision support tools using
system dynamics modelling. Zenodo.
http://doi.org/10.5281/zenodo.5036605

8. introduction
:
PROTIST
:
application
:
conclusion
Phytoplankton Protozooplankton Mixoplankton
1. Photosynthesis
2. Uptake dissolved inorganic
nutrients
1. Capture and assimilate
prey
1. Photosynthesis
2. Uptake dissolved inorganic
nutrients
3. Capture and assimilate
prey
8
A protist community is the base of marine food web and
consists of phyto-, protozoo-, and mixoplankton.

9. introduction
:
PROTIST
:
application
:
conclusion
9
Mixoplankton can be distinguished into four different
types.
9
Constitutive
Mixoplankton
CM
Non-Constitutive
Mixoplankton
NCM
Innate chloroplasts Must aquire photosynthetic capabilities from prey
General
GNCM
plastid Specialist
pSNCM
endosymbiotic
Specialist
eSNCM
e.g. Alexandrium e.g. certain ciliates e.g. Dinophysis Noctiluca
scintillans

10. introduction
:
PROTIST
:
application
:
conclusion
10
Protist has five different functional types with each a
different amount of state variables
Each Protist Functional Type (PFT)
→ Protist C
→ Protist N
→ Protist P
Phototrophic PFTs
→ Protist Chl
Diatom PFT
→ Protist Si

11. introduction
:
PROTIST
:
application
:
conclusion
11
All state variables required
→ 5 Protist Function Types (PFTs)
→ diatom
→ green algae
→ constitutive mixoplankton CM
→ non-constitutive mixoplankton NCM
→ protozooplankton
→ 5 inorganic nutrient state variables
→ 4 particulate organic state variables

12. introduction
:
PROTIST
:
application
:
conclusion
12
Gain fluxes
→ Nutrient uptake

13. introduction
:
PROTIST
:
application
:
conclusion
13
Gain fluxes
→ Photosynthesis

14. introduction
:
PROTIST
:
application
:
conclusion
14
Gain fluxes
→ Grazing

15. introduction
:
PROTIST
:
application
:
conclusion
15
Gain fluxes
→ Grazing
→ Nutrient uptake
→ Photosynthesis

16. introduction
:
PROTIST
:
application
:
conclusion
16
Loss fluxes
→ Respiration (all PFTs)

17. introduction
:
PROTIST
:
application
:
conclusion
17
Loss fluxes
→ Mortality (all PFTs)

18. introduction
:
PROTIST
:
application
:
conclusion
18
Loss fluxes
→ Excretion

19. introduction
:
PROTIST
:
application
:
conclusion
19
Loss fluxes
→ DOC voiding

20. introduction
:
PROTIST
:
application
:
conclusion
20
Loss fluxes
→ Nutrient voiding

21. introduction
:
PROTIST
:
application
:
conclusion
21
Loss fluxes
→ Sedimentation for
diatoms

22. introduction
:
PROTIST
:
application
:
conclusion
22
Loss fluxes
→ Respiration (all PFTs)
→ Mortality (all PFTs)
→ Excretion
→ DOC voiding
→ Nutrient voiding
→ Sedimentation for
diatoms

23. introduction
:
PROTIST
:
application
:
conclusion
23
Conceptual model of
PROTIST

24. introduction
:
PROTIST
:
application
:
conclusion
24
Both sugar kelp as well as the protist community require
access to the dissolved inorganic nutrient pool.
→ Uptakes inorganic nutrients during winter
→ Harvested during summer
→ Competes for dissolved inorganic nutrients
Does the intensification of kelp aquaculture affect the
composition of planktonic protist communities?

25. introduction
:
PROTIST
:
application
:
conclusion
25
We set up a 3D ecological model of the North Sea and ran
two different scenarios.
Zijl, F. et al. (2018). The 3D Dutch Continental Shelf Model – Flexible Mesh (3D DCSM-FM). Deltares rapporte 1220339-000.
PROTIST
Dutch Continental Shelf Model
– Flexible Mesh (DCSM-FM)
D-Water Quality (DELWAQ)
Deltares (2022). D-Water Quality user manual. https://content.oss.deltares.nl/delft3d/manuals/D-Water_Quality_User_Manual.pdf

26. introduction
:
PROTIST
:
application
:
conclusion
26
PROTIST was combined with a seaweed module and two
scenarios were run.
Reference
scenario
Seaweed
scenario
Diatom
Green
algae
Protozoo-
plankton
CM
Seaweed -

27. introduction
:
PROTIST
:
application
:
conclusion
27
In the seaweed scenario, seaweed was seeded in 25 % of
the area of each offshore wind farm.
Modified from Vilmin and Van Duren (2021) Modelling seaweed cultivation on the Dutch continental shelf. Deltares report (https://www.deltares.nl/en/publications/)

28. introduction
:
PROTIST
:
application
:
conclusion
28
The reference scenario manages to capture the timing of
the nutrient peak concentrations well.

29. introduction
:
PROTIST
:
application
:
conclusion
29
These model results visualize the relative difference
between the reference and seaweed scenario.
→ Decrease in DIN and DIP
Surface DIN difference [%] Surface DIP difference [%]

30. introduction
:
PROTIST
:
application
:
conclusion
30
The model results show a relative change in trophic
composition of the protists community in OWF.
→ Relative increase in CM and diatom biomass
Surface CM biomass difference [%] Surface diatom biomass difference [%]

31. introduction
:
PROTIST
:
application
:
conclusion
31
From the 3D model results, it can tentatively be concluded
that
Seaweed aquaculture in the SNS could lead
→ Decrease in DIN and DIP concentrations
Could lead to a
→ Increase of CM biomass
→ Increase of diatom biomass
→ Change in trophic composition of protist
communities
Reference
scenario
Seaweed
scenario
Diatom
Green
algae
Protozoo-
plankton
CM
Seaweed -

32. introduction
:
PROTIST
:
application
:
conclusion
32
PROTIST offers a useful tool to analyze the impact of
anthropogenic changes on marine environments.
Integrated multi-trophic
aquaculture (IMTA)
Offshore wind farms
Planktonic primary production

33. Contact
www.deltares.nl
info@deltares.nl
@deltares
@deltares
linkedin.com/company/deltares
facebook.com/deltaresNL
lisa.schneider@deltares.nl