Community size structure of microbial plankton is associated with functional composition along a resource gradient in mountain lakes

This repository contains codes and data needed to reproduce the analyses and figures of the manuscript:

García-Gómez, G., Sánchez-Hernandez, J., Más Gutiérrez, J.A., & Arranz, I. (2026). Community size structure of microbial plankton is associated with functional composition along a resource gradient in mountain lakes.

Cite the repository as:

García-Gómez, G., Sánchez-Hernandez, J., Más Gutiérrez, J.A., & Arranz, I. (2026). Data, code, and statistical analyses of the manuscript: Community size structure of microbial plankton is associated with functional composition along a resource gradient in mountain lakes. OSF (DOI 10.17605/OSF.IO/2493Q): https://doi.org/10.17605/OSF.IO/2493Q

R scripts

• picoplankton_data_processing.R & nanoplankton_data_processing.R | These scripts contain all the necessary code to process pico- and nanoplankton data, respectively. This workflow obtains raw data from flow cytometry analysis (.fcs files), estimates cell size, and calculates community metrics, including N-M slopes, biovolume, as well as functional dominance variables. Note that functions to convert light-scatter values from flow cytometry data are demonstrated in the supplementary script size_calibration.R (see below).

• env_data_processing.R | This script contains code to process and check data of environmental variables.

• data_analysis.R | This script contains code to reproduce statistical models, model diagnostics, and model selection in this study.

• figures.R | This script contains code to reproduce figures in the paper.

Supplementary scripts

MLE_method.R | This script contains a custom function to estimate N-M slopes through maximum-likelihood method. It was created by Ignasi Arranz using original functions and materials from package sizeSpectra. See: Edwards, A. M. sizeSpectra (Github, 2019); https://github.com/andrew-edwards/sizeSpectra

size_calibration.R | This script contains code to reproduce the conversion from light-scatter values in flow cytometry data (.fcs files) to cell size (expressed here as "equivalent standard diameter" in µm), using calibration beads of known size.

light availability.R | This script contains code to estimate light availability expressed as light irradiance using open-access satellite data.

Data

All raw data used in this study are included in folder raw_data. Please visit Figshare repository to access the data supporting this study: [link]

Microbial plankton

There are two data folders containing all flow cytometry files (.fcs), respectively corresponding to the analysis of picoplankton (VSSC_26032025_25-473) and nanoplankton (FSC_17102024). These datasets contain .fcs files from the cytometry analysis of each lake sample.

Environmental variables

The dataset environmental_data_lakes_2024.csv contains measurements of environmental variables for each sample. Columns in this dataset include:

• ID: unique ID number for data frame rows
• massif: mountain range where each sample was collected
• ID_lake: unique ID number for each lake
• ID_sample: unique ID number for each sample
• lake: lake name (in Spanish)
• habitat: field label to indicate whether sample collection was closer to shore (littoral) or closer to open-waters (pelagic), instead of actual habitat identity
• replicate: sample number within each habitat and lake
• temperature.C: water temperature, in degrees Celsius
• dissolved_oxygen.perc: oxygen saturation, in %
• total_N_ug.L: total nitrogen concentration, in µg/l
• total_P_ug.L: total phosphorus concentration, in µg/l
• nutrilab_label_TN.TP: ID label from nutrient analyses

Lake information

The dataset lakes_location.csv contains data on geographic location (latitude and longitude, in decimal degrees) and elevation (in m.a.s.l.) for each lake investigated here. The fine-resolution satellite data of terrain elevation, which was used to estimate light availability, is also available in the same folder ("appRasterSelectAPIService1764233714639-1101222210.tif").

Size calibration

The folder calibration_beads includes two subfolders, each containing three independent flow cytometry analyses of calibration beads of known diameter respectively for size-ranges of 0.2-2µm and 1-15µm (with their corresponding folders). Cytometer settings were adjusted to improve measuring precision within each size-range by using violet side-scatter and standard side-scatter light, respectively.

Notes

All data processing was carried out in the R software version 4.2.2. The Rcode folder contains the scripts to reproduce the statistical analyses and figures presented in this manuscript. Processed data, model outputs, and figures are already stored in their corresponding folders. These already processed and stored data will be used when rerunning statistical analyses and remaking figures. Note that some of the code requires large memory capacity to process and visualise raw cytometry data (particularly picoplankton_data_processing.R); to avoid this issue, you may use data in folder processed_data. Please do check that package versions in your R session match with package versions used here (and package dependencies, see folder Rsession), so that results are fully reproducible.

R packages

The R packages used for each R script are enlisted in the corresponding R session files (within folder Rsession).

Licence

This repository was provided by the authors under the [to be completed] licence.

Further information

In case of further questions, please contact: Guillermo García-Gómez, email: guillegar.gz@gmail.com