Synchrony and maturation in loop-design grown microbial metacommunities

This repository contains the original cytometric data, R scripts and corresponding input datasets used for the analyses and visualizations in the study “Synchrony and maturation in loop-design grown microbial metacommunities”. The experimental system employed a looped mass-transfer design consisting of five local communities (L1–L5) and one regional pool (R). Three experimental phases were examined: the insular phase (IS, in which no culture exchange among the local communities), the RC10 phase (in which 10% of the culture is recycled from the regional pool to the local communities) and the RC50 phase (in which 50% of the culture is recycled from the regional pool to the local communities). The experiment was organized into three rounds. Round 1 included the IS A, RC10 , RC50 and IS B phases, while Round 2 included the IS I and RC50 I, RC50 II , RC50 III phases. Round 3 immediately followed Round 2 and included the IS II, RC10 , RC50 and IS III. For cytometric data folders Round1,Round2,and Round3: Each bioreactor was sampled, and each sample from the 3 rounds was processed for cytometric analysis to assess microbial community composition and dynamics. A total of 1,226 samples were analyzed, including 365 from a previously published data set (round 1, FlowRepository accession no. FR-FCM-Z3MU) ), and 861 samples, which were collected from the bioreactors in this study in round 2 (513 samples) and round 3 (348 samples). Cells from Round 1, 2 and 3 were fixed with paraformaldehyde (PFA) and stored in 70% ethanol at −20 °C. A defined number of cells was stained with 4',6-diamidino-2-phenylindole (DAPI) for subsequent measurement using a MoFlo Legacy Cell Sorter (Beckman Coulter, Brea, CA, USA). Cytometric data were collected as two-dimensional (2D) dot plots of DAPI fluorescence versus forward scatter (FSC). For Rscripts: The folder FinalRScript is contained two main sections: Maintext contains the R scripts and datasets used for the main text analyses and figures. The first folder, 1_DataSet_Preperation, includes the raw abundance dataset. This abundance table was generated from cytometric data after defining 48 gates, with each gate represented by its relative abundance. The remaining folders are organized by figures. Each figure folder contains the R script and corresponding input dataset required to reproduce the analyses, calculations, and visualizations shown in the main manuscript. Supplementory contains the R scripts and associated input datasets used for the analyses and visualizations presented in the Supplementary Information, organized according to the corresponding supplementary figures. The folder DataSets contains the output datasets used in this study, including relative abundance, absolute cell numbers, dominant SC abundances, abiotic parameters, and removal efficiency data.