DOI: 10.6084/m9.figshare.29954447
title: Nutrient Enrichment and Connectivity Jointly Shape Bacterioplankton Taxonomic and Functional Diversity

description: <b>Data for:</b><b> </b>Kholwadwala, A., E. Katkov, P. Lypaczewski, A. Gonzalez, R. D. H. Barrett, and B. J. Shapiro. 2025. Data from: Nutrient Enrichment and Connectivity Jointly Shape Bacterioplankton Taxonomic and Functional Diversity.<br><br><b>Abstract:</b><b> </b>The increasing and widespread usage of fertilizers and the propensity for these fertilizers to runoff into rivers and lakes poses severe consequences for freshwater communities and ecosystems. It is, therefore, increasingly important to understand the response of freshwater communities and ecosystems to such anthropogenic stressors. Dispersal, an important ecological factor mediated by landscape connectivity, could potentially counteract the impacts of anthropogenic stressors through the reintroduction of communities unperturbed by local stressors. However, this potential has not yet been studied in the context of nutrient stressed natural communities. Here, we investigate the impacts of nutrient enrichment and connectivity on freshwater bacterioplankton communities by subjecting mesocosms stocked with native bacterioplankton communities to different combinations of nutrient enrichment and connectivity (volumes of water transferred between mesocosms). We show that nutrient enrichment at concentrations consistent with those recorded in lakes across the globe strongly structures the bacterioplankton community, favoring nutrient tolerant taxa and depressing taxonomic diversity. Connectivity, however, interacts with nutrient enrichment to restore functional diversity in communities subjected to the highest levels of nutrient stress. Despite the ameliorating effects of dispersal, nutrient enrichment leaves a consistent signature in communities, driving a shift from more heterotrophic to more phototrophic communities. Taken together, our results demonstrate that while nutrient enrichment significantly impacts freshwater bacterioplankton communities, connectivity can help restore functional diversity to a certain extent, broadly demonstrating importance of connectivity in the restoration of ecosystems and communities following anthropogenic disturbances.<br><b>Description of Data:</b><b> </b>We leverage a (semi)natural system of experimental mesocosms with controlled levels of connectivity and nutrient enrichment, along with taxonomic classifications and inferred functional assignments from full-length 16S metabarcoding using nanopore sequencing, to directly evaluate how nutrient enrichment and connectivity shape freshwater bacterioplankton communities.<b>Cluster Scripts</b><b>Description:</b> This folder contains scripts to be run on an computing cluster<b>1_Demultiplexing:</b> This folder contains the custom barcoding arrangement file and custom barcodes file that were used for demultiplexingbarcode_arrs_16s_nbd_hm.toml16s_masked.fasta<b>2_Taxonomic_Assignment</b>: This folder contains the script for the taxonomic classifications of our sequences using EMU (https://github.com/treangenlab/emu)tax_assignment.sh<b>3_Functional_Assignment:</b> This folder contains the script to map taxonomic assignments to functional categories using FAPROTAX (https://pages.uoregon.edu/slouca/LoucaLab/archive/FAPROTAX/lib/php/index.php?section=Instructions)func_assignment.sh<b>Rscript</b><b>Description:</b> This folder contains the R script used for the filtering of the data, the statistical analysis, and the generation of the figuresNutrient_Enrichment_and_Connectivity_Jointly_Shape_Bacterioplankton_Diversity.Rmd<b>Input Data: </b><b>Description:</b> This folder contains the intermediate data and input data for the various scriptsemu_taxonomic_profile.xlsxThe results of the taxonomic classifications from EMUsample_table.xlsxThe sample metadataphyloseq_for_FAPROTAX.tsvThe input file to run FAPROTAXphyloseq_functional_table.xlsxThe results of the functional classifications from FAPROTAX