Dataset: Modeling phytoplankton under multiple frequencies of nutrient supply

Name: R code for a model of phytoplankton community structure under multiple frequencies of pulsed nutrient supply.
Published: 2020-08-11
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.820488.1

Project:

Eating themselves sick? Ecological interactions among a mixotrophic flagellate, its prokaryotic prey, and an ingestible giant virus. (Giant virus ecology)

Principal Investigator:

Kyle F. Edwards (University of Hawaii at Manoa, SOEST)

Contact:

Kyle F. Edwards (University of Hawaii at Manoa, SOEST)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2020-08-11

Restricted:

Validated:

Yes

Current State:

Final no updates expected

R code for a model of phytoplankton community structure under multiple frequencies of pulsed nutrient supply.

Abstract:

R code for a model of phytoplankton community structure under multiple frequencies of pulsed nutrient supply.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2020-08-11	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.820488.1	2021-04-22

Description

A trait-based approach is used to model how phytoplankton community structure might vary when nutrients are supplied periodically at multiple timescales.

Trait variation across phytoplankton ‘species’ is defined by an empirically supported three-way tradeoff between maximum growth rate, specific uptake affinity for phosphate, and internal storage capacity for phosphorus (Edwards et al. 2013).

400 species varying along on this tradeoff plane are initialized in the community, and competition proceeds, with species at very low abundance removed, until the dynamics converge on a periodic attractor.

The frequency and magnitude of nutrient pulses are varied to investigate how community trait structure and diversity respond. Nutrient pulses are reprented as mixing events with water below the surface mixed layer, which simultaneously dilute the phytoplankton populations. Variations in parameter values and the resulting changes in community structure are described in Smith and Edwards (2019).

Data Processing Description

BCO-DMO processing notes:

Linked to the provided R code

Data Files

File

Phytoplankton_Community_Structure_Rcode_Smith_Edwards_2019
filename: Phytoplankton_Community_Structure_Rcode_Smith_Edwards_2019.R

(Octet Stream, 10.34 KB)
MD5:08bfe78a634c2d96e6d8d55292db92c2

R code to model changes in phytoplankton community structure and diversity, based on three traits: maximum growth rate, specific uptake affinity for phosphate, and internal storage capacity for phosphorus. These variables are affected by periodically supplying nutrients at multiple timescales. 

parameter definitions: 

umax = maximum growth rate

Psaff = scaled uptake affinity for phosphorous

vmaxhi = maximum cell-specific phosphate uptake rate when quota is at its minimum

vmaxlo = maximum uptake rate when quota is at its maximum

K = half-saturation constant for phosphate uptake

Q = cellular internal phosphorus concentration

Qmin = minimum phosphorus quota

u.infin=umax*Qmax/(Qmax-Qmin)=theoretical growth rate at inifinite quota

m = instantaneous mortality rate

a = instantaneous mixing rate

d = effective instantaneous mixing/mortality rate for the pulses

S = dissolved phosphorus concentration in water below the mixed layer

f = proportion of phosphorus in dead cells that is instantly remineralized