This data package contains: README.txt (this file) Dolinsek_et_al_2022.zip (Zip file containing all scripts and data used in the publication. Files are organised by figure. Includes copy of readme and file list) File-List.txt (Complete listing of Zip contents) Corresponding publication: ISME COMMUNICATIONS 2, 77 (2022). https://doi.org/10.1038/s43705-022-00160-1 Initial community composition determines the long-term co-existence of microbial cross-feeding cell-types by modulating niche availability Authors: Jan Dolinsek1,2, Josep Ramoneda1,3, David R. Johnson1,* 1Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dubendorf, Switzerland; 2Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH), 8092 Zurich, Switzerland; 3Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA. * Corresponding author (david.johnson@eawag.ch) AUTHOR CONTRIBUTIONS: JD and DRJ conceived the research question, designed the methodology, and designed the experiments. JD performed the experiments, formulated the mathematical model, and performed the model simulations. JD, JR, and DRJ analyzed and interpreted the data. JD and DRJ wrote the manuscript. DRJ initiated and coordinated the project. Instructions for reproducing figures: General: To generate figures, use python script files (.py) in the respective folders. For example, to recreate Figure 3, open "Figure 3/Figure3.py". If you are familiar with python, you will know what to do. If not, please go to https://www.anaconda.com/products/distribution install it, and use the Spyder GUI to open scripts. Press Run File (play button or F5), and you should see the figure pop up (but mind the figure setting in Spyder). Data to generate the figures are deposited in respective folders. For example, Folder Figure 3 has two subfolders, Bioreactor data and Exposure to nitrite. There, the files with data (A1601_10NO3_BCM_pH65.xlsx, A1601_10NO3_BCM_pH75.xlsx, lag_duration_65.xlsx, lag_duration_75.xlsx) are stored. Also, all the growth and evolutionary models (and parameters used) are embedded in the figure scripts. For example, Supplementary figure SI5 is based solely on mathematical model. Therefore, folder Figure SI5 has no subfolders with data, all necessary info to run the model are already within the script. Some figures are hybrid (e.g., Figure 7), showing modeling results and measured data. In such cases, data are included in subfolders (e.g., Bioreactor data). Matlab scripts used to analyze raw colony photographs are in the folder Figure SI3. This folder also includes some photographs of the enclosure used for fluorescent colony photography method. Folder Figure SI8 holds general OD600 growth analysis script, and subfolders including all of the growth curves recorded in the scope of this work. Please refer to figure captions in the manuscript and in the supplementary info for detailed figure description. Sample notation: IFR: We ran two invasion from rare (IFR) experiments, IFR2 with pH = 6.5 and IFR3 with pH = 7.5. We used 96 well plates to grow microbes, the plate setup is described in excel files containing OD600 data (sheet "labels"), these stored in folder \Growth curves data\Experiment Monitoring. Script in the folder Figure SI8 can be reused for OD600 data analysis. Evolved isolates from IFR2 (after 12 transfers at pH = 6.5) are labeled as follows. For example, one evolved isolate is labeled as E1A_9CT12_10NO3_BCM_pH65. This name is composed of: E1A: clone location in the 96 well plates (E1) and phenotype (A) 9CT12: source well (9C) and timepoint (T12) 10NO3: nitrate concentration in the source culture BCM: medium type (BCM is the same as the ACS mineral medium, it is a name often used in the lab) of the source culture pH65: pH value of the source culture Contents of Dolinesk_et_al_2022.zip (abbreviated. see File-List.txt for complete listing) Eawag data package ├── README.txt (this file) ├── File-List.txt ├── Figure 3 │   ├── Bioreactor data │   │   ├── A1601_10NO3_BCM_pH65.xlsx │   │   ├── A1601_10NO3_BCM_pH75.xlsx │   │   ├── FCM_data #42 files │   │   │   ├── 1601Tn7_BCM65_10NO3_050318_1-2018-03-07-150001-1.fcs │   │   │   ├── ... │   │   └── IC_data │   │   ├── 1601Tn7_BCM65_10NO3 #49 files │   │   │   ├── 1601 Tn7 032018 (1).txt │   │   │   ├── ... │   │   │   └── STD #13 files │   │   │   ├── 1601 Tn7 032018 (50).txt │   │   │   └── ... │   │   ├── 1601Tn7_BCM75_10NO3 #84 files │   │   │   ├── -78e38793#15f01c2059a#-7a33_UMIK-METROHM-IC_20171016-155334.txt │   │   │   ├── ... │   │   │   └── STD #13 files │   │   │   ├── -78e38793#15f01c2059a#-7a06_UMIK-METROHM-IC_20171016-155245.txt │   │   │   └── ... │   │   ├── IC_raw_import_and_analysis.m │   │   └── SampleProcessing.m │   ├── Exposure to nitrite │   │   ├── lag_duration_65.xlsx │   │   └── lag_duration_75.xlsx │   └── Figure3.py ├── Figure 4 │   ├── EcoEvo │   │   ├── Invasion_from_rare_pH65.xlsx │   │   └── Invasion_from_rare_pH75.xlsx │   ├── Figure4.py │   └── Fluorescent colony photograps │   ├── IFR2_T0 #24 images │   │   ├── IFR2_T0_7[B-G]_[B,G].jpg │   │   └── IFR2_T0_9[B-G]_[G,R].JPG │   ├── IFR2_T1 #24 images │   │   ├── IFR2_T1_7[B-G]_[B,G].jpg │   │   └── IFR2_T1_9[B-G]_[G,R].JPG │   ├── IFR2_T10 #24 images │   │   ├── IFR2_T10_7[B-G]_[B,G].jpg │   │   └── IFR2_T10_9[B-G]_[G,R].JPG │   ├── IFR2_T11 #24 images │   │   ├── IFR2_T11_7[B-G]_[B,G].jpg │   │   └── IFR2_T11_9[B-G]_[G,R].jpg │   ├── IFR2_T12 #48 images │   │   ├── IFR2_T12_1[A-H]_[B,G,R].jpg │   │   ├── IFR2_T12_7[B-G]_[B,G].jpg │   │   └── IFR2_T12_9[B-G]_[G,R].jpg │   ├── IFR2_T2 #24 images │   │   ├── IFR2_T2_7[B-G]_[B,G].jpg │   │   └── IFR2_T2_9[B-G]_[G,R].JPG │   ├── IFR2_T3 #24 images │   │   ├── IFR2_T3_7[B-G]_[B,G].jpg │   │   └── IFR2_T3_9[B-G]_[G,R].JPG │   ├── IFR2_T4 #48 images │   │   ├── IFR2_T4_1[A-H]_[B,G,R].jpg │   │   ├── IFR2_T4_7[B-G]_[B,G].JPG │   │   └── IFR2_T4_9[B-G]_[G,R].JPG │   ├── IFR2_T5 #24 images │   │   ├── IFR2_T5_7[B-G]_[B,G].JPG │   │   └── IFR2_T5_9[B-G]_[G,R].JPG │   ├── IFR2_T6 #24 images │   │   ├── IFR2_T6_7[B-G]_[B,G].JPG │   │   └── IFR2_T6_9[B-G]_[G,R].JPG │   ├── IFR2_T7 #24 images │   │   ├── IFR2_T7_7[B-G]_[B,G].jpg │   │   └── IFR2_T7_9[B-G]_[G,R].JPG │   ├── IFR2_T8 #48 images │   │   ├── IFR2_T8_1[A-H]_[B,G,R].jpg │   │   ├── IFR2_T8_7[B-G]_[B,G].jpg │   │   └── IFR2_T8_9[B-G]_[G,R].JPG │   ├── IFR2_T9 #24 images │   │   ├── IFR2_T9_7[B-G]_[B,G].jpg │   │   └── IFR2_T9_9[B-G]_[G,R].JPG │   ├── IFR3_T0 #24 images │   │   ├── IFR3_T0_7[B-G]_[B,G].jpg │   │   └── IFR3_T0_9[B-G]_[G,R].jpg │   ├── IFR3_T1 #24 images │   │   ├── IFR3_T1_7[B-G]_[B,G].jpg │   │   └── IFR3_T1_9[B-G]_[G,R].jpg │   ├── IFR3_T2 #24 images │   │   ├── IFR3_T2_7[B-G]_[B,G].jpg │   │   └── IFR3_T2_9[B-G]_[G,R].jpg │   ├── IFR3_T3 #24 images │   │   ├── IFR3_T3_7[B-G]_[B,G].jpg │   │   └── IFR3_T3_9[B-G]_[G,R].jpg │   ├── IFR3_T4 #24 images │   │   ├── IFR3_T4_7[B-G]_[B,G].jpg │   │   └── IFR3_T4_9[B-G]_[G,R].jpg │   ├── IFR3_T5 #24 images │   │   ├── IFR3_T5_7[B-G]_[B,G].jpg │   │   └── IFR3_T5_9[B-G]_[G,R].jpg │   ├── IFR3_T6 #48 images │   │   ├── IFR3_T6_1[A-H]_[B,G,R].jpg │   │   ├── IFR3_T6_7[B-G]_[B,G].jpg │   │   └── IFR3_T6_9[B-G]_[G,R].jpg │   └── IFR3_T7 #24 images │   ├── IFR3_T7_7[B-G]_[B,G].jpg │   └── IFR3_T7_9[B-G]_[G,R].jpg ├── Figure 5 │   ├── Evolved clone collection │   │   ├── IFR_clones_sorted_ratecorrected.xlsx │   │   └── Support Analysis.py │   ├── Figure5.py │   └── OD600_data #11 .xlsx files │   ├── 070917_JD_65_fresh_10mMNO3_IFR2_1ET12_MAXLIB.xlsx │   └── ... ├── Figure 6 │   ├── Evolved clone collection │   │   ├── IFR_clones_sorted_ratecorrected.xlsx │   │   └── Support Analysis.py │   ├── Figure6.py │   └── OD600_data #11 .xlsx files │   ├── 070917_JD_65_fresh_10mMNO3_IFR2_1ET12_MAXLIB.xlsx │   └── ... ├── Figure 7 │   ├── Bioreactor data │   │   ├── E1A_9CT12_10NO3_BCM_pH65.xlsx │   │   ├── FCM_data #48 files │   │   │   ├── 9CT12_1A_BCM65_10NO3_1-2018-03-07-112824-4.fcs │   │   │   └── ... │   │   └── IC_data #50 .txt files │   │   ├── 9CT12 1A, 1#25 in 0.1% GTA, 10 mM NO3, BCM pH6.5 10_UMIK-SPECORD300_20180304-200411.txt │   │   ├── ... │   │   ├── 9CT12_1A_BCM65_10NO3 (all).mat │   │   ├── IC_raw_import_and_analysis.m │   │   ├── STD #13 .txt files │   │   │   ├── BCM pH6.5 0 mM STD_UMIK-SPECORD300_20180307-093707.txt │   │   │   └── ... │   │   └── SampleProcessing.m │   └── Figure7.py ├── Figure SI1 │   ├── FigureSI1.py │   └── Growth curves data │   └── Founder Screening │   ├── 080916_JD_NO3_160x_plate1.xlsx │   ├── 090916_JD_O2_160x_plate1.xlsx │   ├── Analysis_080916_JD_160x_O2_plate1.m │   ├── Analysis_090916_JD_160x_NO3_plate1.m │   ├── Founders - Growth on NO3 unprocessed.svg │   ├── Founders - Growth on O2 and NO3.svg │   ├── Founders - Growth on O2 unprocessed.svg │   ├── data_correction.m │   ├── growth_rate_window_fit_data.m │   ├── plot_OD_vs_t.m │   ├── plot_mu_vs_OD.m │   └── read_raw_data.m ├── Figure SI2 │   ├── Bioreactor data │   │   ├── A1601_10NO3_BCM_pH65.xlsx │   │   ├── A1601_10NO3_BCM_pH75.xlsx │   │   ├── A1601_5NO3_BCM_pH65.xlsx │   │   ├── FCM_data #42 .fcs files, 3 .c6 files │   │   │   ├── 1601Tn7_BCM65_10NO3_050318_1-2018-03-07-150001-1.fcs │   │   │   ├── ... │   │   │   ├── 2017-10-04_1601Tn7_BCM6.5_5mMNO3_27092017_1to600_50ul.c6 │   │   │   └── ... │   │   └── IC_data │   │   ├── 1601Tn7_BCM65_10NO3 #49 .txt files │   │   │   ├── 1601 Tn7 032018 (1).txt │   │   │   ├── ... │   │   │   └── STD #13 .txt files │   │   │   ├── 1601 Tn7 032018 (50).txt │   │   │   └── ... │   │   ├── 1601Tn7_BCM65_5NO3 #81 .txt files │   │   │   ├── -78e38793#15f01c2059a#-7574_UMIK-METROHM-IC_20171016-153136.txt │   │   │   ├── ... │   │   │   └── STD #9 .txt files │   │   │   ├── -78e38793#15f01c2059a#-7556_UMIK-METROHM-IC_20171016-153104.txt │   │   │   └── ... │   │   ├── 1601Tn7_BCM75_10NO3 #84 .txt files │   │   │   ├── -78e38793#15f01c2059a#-7a33_UMIK-METROHM-IC_20171016-155334.txt │   │   │   ├── ... │   │   │   └── STD #13 .txt files │   │   │   ├── -78e38793#15f01c2059a#-7a06_UMIK-METROHM-IC_20171016-155245.txt │   │   │   └── ... │   │   ├── IC_raw_import_and_analysis.m │   │   └── SampleProcessing.m │   └── FigureSI2.py ├── Figure SI3 │   ├── ColonyAnalysis_RED_and_BLUE_OK.m │   ├── IMG_0811.JPG │   ├── IMG_0814.JPG │   ├── IMG_0820.JPG │   ├── Zoomin1.jpg │   ├── Zoomin2.jpg │   └── Zoomout.jpg ├── Figure SI4 │   ├── FigureS4.py │   └── Growth curves data │   ├── NO3 vs pH vs NO2 availability │   │   └── 150916_JD_NO3_1601Tn7.xlsx │   └── Sequenced Strains │   └── OD600_sequencedStrains.xlsx ├── Figure SI5 │   └── FigureSI5.py ├── Figure SI6 │   ├── Exposure to nitrite │   │   └── NO2_availablity_data.xlsx │   ├── FigureSI6.py │   └── OD600_data #19 .xlsx files │   ├── 011216_JD_6.5_10mMNO3_IFR2_T5_to_T6.xlsx │   └── ... ├── Figure SI7 #12 images │   ├── IFR2_T0_7B_B.JPG │   └── ... ├── Figure SI8 │   ├── Growth curves data │   │   ├── Experiment Monitoring #19 .xlsx files │   │   │   ├── 011216_JD_6.5_10mMNO3_IFR2_T5_to_T6.xlsx │   │   │   └── ... │   │   ├── Founder Screening │   │   │   ├── 080916_JD_NO3_160x_plate1.xlsx │   │   │   └── 090916_JD_O2_160x_plate1.xlsx │   │   ├── NO3 vs pH vs NO2 availability │   │   │   └── 150916_JD_NO3_1601Tn7.xlsx │   │   ├── Population Analysis │   │   │   ├── 070917_JD_65_fresh_10mMNO3_IFR2_1ET12_MAXLIB.xlsx │   │   │   ├── 07112017_JD_65_fresh_10mMNO3_IFR2_9CT12_MAXLIB_rere.xlsx │   │   │   ├── 090218_JD_65_fresh_10mMNO3_IFR2_T12_1D_MAXLIB_re.xlsx │   │   │   ├── 10102017_JD_65_fresh_10mMNO3_IFR2_9FT12_MAXLIB_re.xlsx │   │   │   ├── 13102017_JD_65_fresh_10mMNO3_IFR2_9GT12_MAXLIB_re.xlsx │   │   │   ├── 14112017_JD_75_fresh_10mMNO3_IFR2_1FT12_MAXLIB.xlsx │   │   │   ├── 15112017_JD_65_fresh_10mMNO3_IFR2_1FT12_MAXLIB.xlsx │   │   │   ├── 17102017_JD_65_fresh_10mMNO3_IFR2_9DT12_MAXLIB_re.xlsx │   │   │   ├── 250717_JD_65_fresh_10mMNO3_IFR2_9ET12_MAXLIB.xlsx │   │   │   ├── 290917_JD_65_fresh_10mMNO3_IFR2_T12_1C_MAXLIB_re.xlsx │   │   │   └── 31102017_JD_65_fresh_10mMNO3_IFR2_9BT12_MAXLIB_rere.xlsx │   │   └── Sequenced Strains │   │   └── OD600_sequencedStrains.xlsx │   └── OD600 analysis.py ├── Figure SI9 │   └── FigureSI9.py └── Table S2    ├── Microbe.1.0.xlsx    ├── Microbe.1.0_DJ_080721.xlsx    ├── SRA_metadata.xlsx    └── SRA_metadata_DJ_080721.xlsx 76 directories, 1356 files