DOI: 10.5061/dryad.866t1g1tr
title: Data from: Microbial population dynamics decouple growth response from environmental nutrient concentration

description: To explore the diversity of microbial growth responses, we have compiled
 247 measurements of half-saturation concentrations K and maximum growth
 rates gmax from previously-published studies (see Methods). The data
 includes a wide range of resources, including sources of carbon, nitrogen,
 phosphorus, metals, and vitamins, with phosphate, glucose, and nitrate
 having the largest number of measurements due to their emphasis in marine
 and laboratory systems.  Organisms include prokaryotes and
 eukaryotes as well as autotrophs and heterotrophs. This data has been
 analyzed in a companion research article. For data plots and a discussion
 of results, please refer to: Fink, Justus Wilhelm, Noelle A. Held, and
 Michael Manhart. “Microbial Population Dynamics Decouple Growth Response
 from Environmental Nutrient Concentration.” Proceedings of the National
 Academy of Sciences 120, no. 2 (January 10, 2023).
 https://doi.org/10.1073/pnas.2207295120.
description: We collected measurements of Monod model parameters
 (half-saturation concentration K and maximum growth rate gmax) through a
 targeted literature search that included prior surveys and reviews [1, 2],
 the phytoplankton trait database [3], as well as original research papers.
 In all but two cases, we traced data from surveys and reviews back to
 their original papers, which we report in Dataset S1 (sheet 1).
 <br><br>We included only experiments that directly measured
 population growth rates, rather than nutrient uptake rates or respiration.
 We excluded measurements where the actual limiting resource was unclear,
 such as measurements in rich medium with added glucose. Where possible, we
 checked the raw data of growth rate over resource concentrations to
 determine if the focal resource concentration was measured up to
 saturation and had sufficient sampling of concentrations around $K$.  For
 a subset of measurements of <em>E.coli </em>on glucose, we
 also checked for the concentration of a nitrogen source to determine the
 relative impact of colimitation (Dataset S1, sheet 2). To assess the
 effect of pre-acclimation, we focused on a subset of isolates with paired
 measurements under different regimes of acclimation (Dataset S1, sheet 3).
 If the original K value was reported as weight per volume, we converted
 these into units of micromolar (µM) using the calculated molecular weight
 of the compound's chemical formula. We preserved significant digits
 from the original studies. [1]
 Kovárová-Kovar, Karin, and Thomas Egli. “Growth Kinetics of Suspended
 Microbial Cells: From Single-Substrate-Controlled Growth to
 Mixed-Substrate Kinetics.” <em>Microbiology and Molecular Biology
 Reviews</em> 62, no. 3 (1998): 646–66. https://doi.org/10.1128/MMBR.62.3.646-666.1998 [2] Owens, J.D., and J.D. Legan. “Determination of the Monod Substrate Saturation Constant for Microbial Growth.” <em>FEMS Microbiology Letters</em> 46, no. 4 (1987): 419–32. https://doi.org/10.1111/j.1574-6968.1987.tb02478.x. [3] Edwards, Kyle F., Christopher A. Klausmeier, and Elena Litchman. “Nutrient Utilization Traits of Phytoplankton.” <em>Ecology</em> 96, no. 8 (2015): 2311–2311. https://doi.org/10.1890/14-2252.1.
description: The datafile can be opened with Microsoft Excel or the free
 open-source alternative Libre Office. 
 To open the dataset in Python, we recommend the package pandas. We give a
 short example how to load this dataset with pandas in the accompanying
 file 'README.md'.