DOI: 10.5281/zenodo.14762144
title: National-scale biogeography and function of river and stream bacterial biofilm communities

description: Supplementary data associated with 'National-scale biogeography and function of river and stream bacterial biofilm communities'.

R scripts for data analysis and visualisation of this dataset are available on GitHub at: https://github.com/amycthorpe/biofilm_MAG_analysis.

Snakemake workflows to generate the results are available on GitHub at: https://github.com/amycthorpe/metag_analysis_EA and https://github.com/amycthorpe/EA_metag_post_analysis.

Metagenomic reads and assembled MAGs have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB85861.

Environmental metadata:



water_chem.csv - water chemistry associated with each sample [source: https://environment.data.gov.uk/water-quality/view/landing]



values are the minimum, maximum and mean calculated for each variable across a 3-month period prior to sampling

times are the number of measurements taken during the 3-month period

alkalinity to pH 4.5 as CaCO3 (mg L-1)

ammonia unionised as N (mg L-1)

ammonical nitrogen as N (mg L-1)

dissolved organic carbon (mg L-1)

chloride ion (mg L-1)

conductivity at 25 °C

nitrate as N (mg L-1)

nitrite as N (mg L-1)

total oxidised nitrogen (mg L-1)

total nitrogen (mg L-1)

reactive orthophosphate (mg L-1)

dissolved oxygen (mg L-1)

dissolved oxygen (% saturation)

total phosphorus (mg L-1)

reactive silica as SiO2 (mg L-1)

water temperature (°C)

pH



catchment_land_cover.csv - percentage of upstream catchment covered by each land cover type [source: https://www.ceh.ac.uk/data/ukceh-land-cover-maps]

catchment_geology.csv - percentage of upstream catchment covered by each geology type [source: https://www.bgs.ac.uk/datasets/bgs-geology-250k]

catchment_chars.csv - characteristics of the upstream catchment, includes:



altitude in m 

catchment area in sqkm [source: https://catalogue.ceh.ac.uk/cmp/documents]

strahler stream order [source: https://www.ordnancesurvey.co.uk/products/os-open-rivers]

river depth and width in m [source: https://doi.org/10.5285/8df65124-68e9-4c68-8659-1c6b82c735e9]

average shade [source: https://data.catchmentbasedapproach.org/maps/theriverstrust::riparian-shade-england]

population equivalent wastewater treatment plant (WWTP) load in sqkm [source: https://www.data.gov.uk/dataset/0f76a1c3-1368-476b-a4df-7ef32bfd9a8b/urban-waste-water-treatment-directive-treatment-plants]




Metagenome assembled genomes (MAGs):



finalbins_coverage.csv - coverage of MAGs per sample

checkm_gtdb.csv - statistics calculated with CheckM2 for each MAG and MAG taxonomy with the GTDB-tk database

levins_median.csv - Levins' niche breadth index (Bn) calculated for each MAG, the associated P value (P.val) and adjusted P value (P.adj), N denoting above threshold of quantification (Below.NOQ), and identification as generalist or specialist (category, Bn > median Bn = generalist, Bn < median Bn = specialist)

singlem_results.csv - proportion of metagenomic reads assigned to bacteria, archaea and eukaryotes calculated with SingleM

env_with_seq_accessions.csv - ENA accessions for metagenomic reads

mag_accessions.csv - ENA accessions for dereplicated MAGs


Metabolic and functional traits:



metabolic_results.csv - presence of metabolic pathways in the MAGs generated using METABOLIC

metabolishmm_results.csv - presence of metabolic pathways in the MAGs generated using metabolisHMM

microtrait_results.csv - presence of functional traits identified in the MAGs using microTrait

biofilm_KO_counts.csv - counts of biofilm-associated KOs identified per MAG using MicrobeAnnotator

KO_list_pathways.csv - list of KOs in biofilm-associated pathways


Environmental drivers:



varPart.csv - results of variance partitioning between MAGs and environmental metadata

correlations.csv - pearson correlation coefficients (r_value, p_value and significance level) between environmental metadata and bacterial phyla.

envfit.csv - results from vegan envfit() function for NMDS analysis of MAG relative abundance and environmental metadata.


Citation:

Thorpe, A.C. et al. National-scale biogeography and function of river and stream bacterial biofilm communities. Nature Communications. 16, 10571 (2025). https://doi.org/10.1038/s41467-025-65620-3