Journal cover Journal topic
Geoscientific Model Development An interactive open-access journal of the European Geosciences Union
Geosci. Model Dev., 9, 4071-4085, 2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
Model description paper
14 Nov 2016
PhytoSFDM version 1.0.0: Phytoplankton Size and Functional Diversity Model
Esteban Acevedo-Trejos1, Gunnar Brandt1,a, S. Lan Smith2, and Agostino Merico1,3 1Systems Ecology Group, Leibniz Center for Tropical Marine Ecology, Fahrenheitstrasse 6, 28359 Bremen, Germany
2Marine Ecosystem Dynamics Research Group, Research and Development Center for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokohama, Japan
3Faculty of Physics & Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
acurrent address: Brockmann Consult, Max-Planck-Str. 7, 21052 Geesthacht, Germany
Abstract. Biodiversity is one of the key mechanisms that facilitate the adaptive response of planktonic communities to a fluctuating environment. How to allow for such a flexible response in marine ecosystem models is, however, not entirely clear. One particular way is to resolve the natural complexity of phytoplankton communities by explicitly incorporating a large number of species or plankton functional types. Alternatively, models of aggregate community properties focus on macroecological quantities such as total biomass, mean trait, and trait variance (or functional trait diversity), thus reducing the observed natural complexity to a few mathematical expressions. We developed the PhytoSFDM modelling tool, which can resolve species discretely and can capture aggregate community properties. The tool also provides a set of methods for treating diversity under realistic oceanographic settings. This model is coded in Python and is distributed as open-source software. PhytoSFDM is implemented in a zero-dimensional physical scheme and can be applied to any location of the global ocean. We show that aggregate community models reduce computational complexity while preserving relevant macroecological features of phytoplankton communities. Compared to species-explicit models, aggregate models are more manageable in terms of number of equations and have faster computational times. Further developments of this tool should address the caveats associated with the assumptions of aggregate community models and about implementations into spatially resolved physical settings (one-dimensional and three-dimensional). With PhytoSFDM we embrace the idea of promoting open-source software and encourage scientists to build on this modelling tool to further improve our understanding of the role that biodiversity plays in shaping marine ecosystems.

Citation: Acevedo-Trejos, E., Brandt, G., Smith, S. L., and Merico, A.: PhytoSFDM version 1.0.0: Phytoplankton Size and Functional Diversity Model, Geosci. Model Dev., 9, 4071-4085,, 2016.
Publications Copernicus
Short summary
Marine phytoplankton plays a prominent role in regulating Earth’s climate. Numerical models are important tools that help us investigate the interactions between these microbes and their environment. We proposed PhytoSFDM as an open-source model to quantify size structure and functional diversity of marine phytoplankton communities. This tool allows us, in a manageable and computationally efficient way, to study patterns in planktonic ecosystems and their feedbacks with a changing environment.
Marine phytoplankton plays a prominent role in regulating Earth’s climate. Numerical models...