National-scale biogeography and function of river and stream bacterial biofilm communities

Supplementary data associated with 'National-scale biogeography and function of river and stream bacterial biofilm communities'. Preprint is available at: https://doi.org/10.1101/2025.03.05.641783.

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.

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

water temperature (°C)

pH

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

conductivity at 25 °C

dissolved oxygen (DO, mg L-1)

dissolved organic carbon (DOC, mg L-1)

reactive orthophosphate (mg L-1)

nitrate as N (nitrate-N, mg L-1)

nitrite as N (nitrite-N, mg L-1)

ammoniacal nitrogen as N (ammonia-N, mg L-1)

reactive silica as SiO2 (mg L-1) 

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

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.