This repository contains all code and data necessary to reproduce the results presented in the manuscript 'Environment-organism feedbacks drive changes in ecological interactions', by Oliver J. Meacock and Sara Mitri.
It contains two directories, Data and Models, which respectively contain raw measurements and R scripts for their analysis, and Jupyter notebooks containing code for simulating OE systems.
Contains the following sub-folders:
- Intra-specific interactions: contains original .xpt files (generated by BioTek Gen5™ software) of growthcurves (XXX_Ct_Proline_Ampicillin_PopulationDependence.xpt) and corresponding .xlsx files containing exported values. Analyse_09_23_Timecourses_Amp_Pro_Ct_Triplicate.R can be used to analyse and plot these datasets.
- MICs: contains raw OD measurements for calculating MICs of ampicillin (07_10_23_Ct_MICs.xpt), as well as a corresponding .xlsx file containing exported values. Analyse_09_23_Ct_MICs.R can be used to plot these datasets.
- Beta-lactamase assays: contains raw spectrophotometer measurements of nitrocefin hydrolysis rate for each sampled timepoint (16_02_23_Ct_At_BetaLactamaseAssay_t=X.xpt), along with raw exports of the data to .xlsx format. 'ResultsWorkable.xlsx' contains this data converted to a human-readable format, and also includes CFU data for the same experiment. Individual sheets in this workbook contain the following:
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'Ct' and 'At': Contain annotated spectrophotometer absorbance curves at 490nm, the peak of the absorbance spectrum of hydrolysed nitrocephin. The two sheets indicate data for flasks containing Comamonas testosteroni and Agrobacterium tumefaciens. Annotations indicate the timepoint of the sample in hours, the biological replicate ID (different numbers representing samples grown in separate flasks), technical replicate ID (different numbers representing different samples taken from a flask with a given biological replicate ID) and whether the sample contained ampicillin during culturing. Includes calculations of estimated enzyme concentrations.
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'Standard curves': Calculation of the extinction coefficient of hydrolysed nitrocefin based on samples of known concentration.
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'Blank wells': Absorbance curves for blank wells (i.e. wells containing only nitrocefin). Used for calculating the detection limit.
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'Ct CFUs' and 'At CFUs': Estimated density of colony forming units (CFUs) in flasks at the indicated timepoints.
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'R formatting': Data from 'Ct' and 'Ct CFUs' consolidated to facilitate plotting in R.
See https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/312/635/mak545pis-mk.pdf for further details of the nitrocefin assay and calculations involved. 'Plot_16_02_23_BetaLactamaseAssays.R' reads the data from this workbook and plots it.
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Contains three Jupyter notebooks, Degrader-crossfeeder model.ipynb, Toxin-nutrient model.ipynb and TilmanSuccession.ipynb that can be used to reproduce the simulations and figures presented in the manuscript. More exact specifications of the code used to generate each figure is given in the notebooks.
Meacock, O.J. and Mitri, S. Environment-organism feedbacks drive changes in ecological interactions, bioRxiv (2023) https://doi.org/10.1101/2023.10.31.565024