ABSTRACT Lakes are heterogeneous ecosystems inhabited by a rich microbiome whose genomic diversity is poorly defined. We present a continental-scale study of metagenomes representing 6.5

million km2 of the most lake-rich landscape on Earth. Analysis of 308 Canadian lakes resulted in a metagenome-assembled genome (MAG) catalogue of 1,008 mostly novel bacterial genomospecies.

Lake trophic state was a leading driver of taxonomic and functional diversity among MAG assemblages, reflecting the responses of communities profiled by 16S rRNA amplicons and gene-centric

metagenomics. Coupling the MAG catalogue with watershed geomatics revealed terrestrial influences of soils and land use on assemblages. Agriculture and human population density were drivers

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VIEWED BY OTHERS DEPTH-DISCRETE METAGENOMICS REVEALS THE ROLES OF MICROBES IN BIOGEOCHEMICAL CYCLING IN THE TROPICAL FRESHWATER LAKE TANGANYIKA Article Open access 09 February 2021 TWO

DECADES OF BACTERIAL ECOLOGY AND EVOLUTION IN A FRESHWATER LAKE Article 03 January 2025 A GENOME AND GENE CATALOG OF THE AQUATIC MICROBIOMES OF THE TIBETAN PLATEAU Article Open access 16

February 2024 DATA AVAILABILITY Raw metagenome reads were archived in the European Nucleotide Archive under study accession PRJEB29238. Metagenome co-assemblies were deposited and annotated

at the Joint Genome Institute (JGI) Genomes OnLine Database (GOLD) under study accession Gs0136026 and analysis projects Ga0495746 (Boreal/Taiga Cordilleras), Ga0495744 (Montane Cordillera),

Ga0495745 (Pacific Maritime), Ga0495743 (Taiga Plains), Ga0485099 (Semi-Arid Plateaux), Ga0485102 (Boreal Plains), Ga0485100 (Prairies), Ga0364548 (Mixedwood Plains), Ga0373103 (Boreal

Shield), Ga0372599 (Atlantic Highlands) and Ga0372598 (Atlantic Maritime). MAGs from co-assemblies and associated annotations were deposited in Dryad112 and at the European Nucleotide

Archive under study accession PRJEB62834. Publicly available datasets used in this study include HydroLakes v.1.0 (https://www.hydrosheds.org/products/hydrolakes), SoilGrids250m

(https://www.soilgrids.org/), ERA5-Land (https://doi.org/10.24381/cds.e2161bac), Canada Ecozones v.5b (https://ccea-ccae.org/ecozones-downloads/), Rfam v.14.2

(https://ftp.ebi.ac.uk/pub/databases/Rfam/14.2/), Transporter Classification Database downloaded on 27 January 2021 (https://tcdb.org/public/tcdb), dbCAN2 HMMdb v.9

(https://bcb.unl.edu/dbCAN2/download/dbCAN-HMMdb-V9.txt), GTDB r95 (https://data.gtdb.ecogenomic.org/releases/release95/) and DADA2-formatted 16S rRNA gene sequences

(GTDB_bac120_arc122_ssu_r95.fa.gz; https://doi.org/10.5281/zenodo.3951383). Source data are provided with this paper. CODE AVAILABILITY Scripts associated with this study are available at

https://github.com/rebeccagarner/lakepulse_mags. CHANGE HISTORY * _ 11 OCTOBER 2023 A Correction to this paper has been published: https://doi.org/10.1038/s41564-023-01515-7 _ REFERENCES *

Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. _Microbiol. Mol. Biol. Rev._ 75, 14–49 (2011). Article

  CAS  PubMed  PubMed Central  Google Scholar  * Pernthaler, J. Competition and niche separation of pelagic bacteria in freshwater habitats. _Environ. Microbiol._ 19, 2133–2150 (2017).

Article  CAS  PubMed  Google Scholar  * Bertilsson, S. & Mehrshad, M. in _Encyclopedia of Inland Waters_ (eds Mehner, T. & Tockner, K.) 601–615 (Elsevier, 2022). * Kratz, T. K.,

MacIntyre, S. & Webster, K. E. in _Ecosystem Function in Heterogeneous Landscapes_ (eds Lovett, G. M. et al.) 329–347 (Springer, 2005). * Tranvik, L. J. et al. Lakes and reservoirs as

regulators of carbon cycling and climate. _Limnol. Oceanogr._ 54, 2298–2314 (2009). Article  CAS  Google Scholar  * Williamson, C. E., Dodds, W., Kratz, T. K. & Palmer, M. A. Lakes and

streams as sentinels of environmental change in terrestrial and atmospheric processes. _Front. Ecol. Environ._ 6, 247–254 (2008). Article  Google Scholar  * Grossart, H., Massana, R.,

McMahon, K. D. & Walsh, D. A. Linking metagenomics to aquatic microbial ecology and biogeochemical cycles. _Limnol. Oceanogr._ 65, S2–S20 (2020). Article  CAS  Google Scholar  *

O’Reilly, C. M. et al. Rapid and highly variable warming of lake surface waters around the globe. _Geophys. Res. Lett._ 42, 10773–10781 (2015). Google Scholar  * Smith, V. H. &

Schindler, D. W. Eutrophication science: where do we go from here? _Trends Ecol. Evol._ 24, 201–207 (2009). Article  PubMed  Google Scholar  * Jane, S. F. et al. Widespread deoxygenation of

temperate lakes. _Nature_ 594, 66–70 (2021). Article  CAS  PubMed  Google Scholar  * Dugan, H. A. et al. Lakes at risk of chloride contamination. _Environ. Sci. Technol._ 54, 6639–6650

(2020). Article  CAS  PubMed  Google Scholar  * Reid, A. J. et al. Emerging threats and persistent conservation challenges for freshwater biodiversity. _Biol. Rev._ 94, 849–873 (2019).

Article  PubMed  Google Scholar  * Sheridan, E. A. et al. Plastic pollution fosters more microbial growth in lakes than natural organic matter. _Nat. Commun._ 13, 4175 (2022). Article  CAS 

PubMed  PubMed Central  Google Scholar  * Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. _Nature_ 428, 37–43 (2004).

Article  CAS  PubMed  Google Scholar  * Hug, L. A. et al. A new view of the tree of life. _Nat. Microbiol._ 1, 16048 (2016). Article  CAS  PubMed  Google Scholar  * Cabello-Yeves, P. J. et

al. Genomes of novel microbial lineages assembled from the sub-ice waters of Lake Baikal. _Appl. Environ. Microbiol._ 84, e02132-17 (2018). Article  PubMed  Google Scholar  * Okazaki, Y.,

Nakano, S., Toyoda, A. & Tamaki, H. Long-read-resolved, ecosystem-wide exploration of nucleotide and structural microdiversity of lake bacterioplankton genomes. _mSystems_ 7, e0043322

(2022). Article  PubMed  Google Scholar  * Mehrshad, M. et al. Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi. _Microbiome_ 6, 176 (2018). Article 

PubMed  PubMed Central  Google Scholar  * Arora-Williams, K. et al. Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake. _Microbiome_ 6, 165 (2018).

Article  PubMed  PubMed Central  Google Scholar  * Tran, P. Q. et al. Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake

Tanganyika. _ISME J._ 15, 1971–1986 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  * Rodriguez‐R, L. M., Tsementzi, D., Luo, C. & Konstantinidis, K. T. Iterative

subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences. _Environ. Microbiol._ 22, 3394–3412 (2020). Article  PubMed 

Google Scholar  * Kavagutti, V. S. et al. High-resolution metagenomic reconstruction of the freshwater spring bloom. _Microbiome_ 11, 15 (2023). Article  PubMed  PubMed Central  Google

Scholar  * Tully, B. J., Graham, E. D. & Heidelberg, J. F. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. _Sci. Data_ 5, 170203 (2018). Article 

CAS  PubMed  PubMed Central  Google Scholar  * Anantharaman, K. et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. _Nat.

Commun._ 7, 13219 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  * Almeida, A. et al. A new genomic blueprint of the human gut microbiota. _Nature_ 568, 499–504 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar  * Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S. & Kyrpides, N. C. New insights from uncultivated genomes of the global human

gut microbiome. _Nature_ 568, 505–510 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  * Pasolli, E. et al. Extensive unexplored human microbiome diversity revealed by over

150,000 genomes from metagenomes spanning age, geography, and lifestyle. _Cell_ 176, 649–662.e20 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  * Nayfach, S. et al. A genomic

catalog of Earth’s microbiomes. _Nat. Biotechnol._ 39, 499–509 (2021). Article  CAS  PubMed  Google Scholar  * Buck, M. et al. Comprehensive dataset of shotgun metagenomes from oxygen

stratified freshwater lakes and ponds. _Sci. Data_ 8, 131 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  * Messager, M. L., Lehner, B., Grill, G., Nedeva, I. & Schmitt, O.

Estimating the volume and age of water stored in global lakes using a geo-statistical approach. _Nat. Commun._ 7, 13603 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  * Huot,

Y. et al. The NSERC Canadian Lake Pulse Network: a national assessment of lake health providing science for water management in a changing climate. _Sci. Total Environ._ 695, 133668 (2019).

Article  CAS  PubMed  Google Scholar  * Kraemer, S. A. et al. A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities. _ISME J._ 14, 3011–3023

(2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Wight, J., Varin, M.-P., Robertson, G. J., Huot, Y. & Lang, A. S. Microbiology in the field: construction and validation

of a portable incubator for real-time quantification of coliforms and other bacteria. _Front. Public Health_ 8, 607997 (2020). Article  PubMed  PubMed Central  Google Scholar  * Garner, R.

E., Gregory-Eaves, I. & Walsh, D. A. Sediment metagenomes as time capsules of lake microbiomes. _mSphere_ 5, e00512-20 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Garner, R. E. et al. Protist diversity and metabolic strategy in freshwater lakes are shaped by trophic state and watershed land use on a continental scale. _mSystems_ 7, e0031622 (2022).

Article  PubMed  Google Scholar  * MacKeigan, P. W. et al. Comparing microscopy and DNA metabarcoding techniques for identifying cyanobacteria assemblages across hundreds of lakes. _Harmful

Algae_ 113, 102187 (2022). Article  CAS  PubMed  Google Scholar  * Oliva, A., Garner, R. E., Walsh, D. & Huot, Y. The occurrence of potentially pathogenic fungi and protists in Canadian

lakes predicted using geomatics, in situ and satellite-derived variables: towards a tele-epidemiological approach. _Water Res._ 209, 117935 (2021). Article  PubMed  Google Scholar  *

Griffiths, K. et al. Pervasive changes in algal indicators since pre-industrial times: a paleolimnological study of changes in primary production and diatom assemblages from ~200 Canadian

lakes. _Sci. Total Environ._ 838, 155938 (2022). Article  CAS  PubMed  Google Scholar  * Kraemer, S. A., Barbosa da Costa, N., Oliva, A., Huot, Y. & Walsh, D. A. A resistome survey

across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use. _Front. Microbiol._ 13, 995418 (2022). Article  PubMed  PubMed Central 

Google Scholar  * Oliva, A. et al. Geospatial analysis reveals a hotspot of fecal bacteria in Canadian prairie lakes linked to agricultural non-point sources. _Water Res._ 231, 119596

(2023). Article  CAS  PubMed  Google Scholar  * Sánchez Schacht, J. R., MacKeigan, P. W., Taranu, Z. E., Huot, Y. & Gregory-Eaves, I. Agricultural land use and lake morphology explain

substantial variation in water quality across Canada. Preprint at _bioRxiv_ https://doi.org/10.1101/2022.08.29.505280 (2023). * Albertsen, M. et al. Genome sequences of rare, uncultured

bacteria obtained by differential coverage binning of multiple metagenomes. _Nat. Biotechnol._ 31, 533–538 (2013). Article  CAS  PubMed  Google Scholar  * Bowers, R. M. et al. Minimum

information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. _Nat. Biotechnol._ 35, 725–731 (2017). Article  CAS  PubMed  PubMed

Central  Google Scholar  * Fernández-Gómez, B. et al. Ecology of marine Bacteroidetes: a comparative genomics approach. _ISME J._ 7, 1026–1037 (2013). Article  PubMed  PubMed Central  Google

Scholar  * De Corte, D. et al. Metagenomic insights into zooplankton-associated bacterial communities. _Environ. Microbiol._ 20, 492–505 (2018). Article  PubMed  Google Scholar  * Ezzedine,

J. A., Desdevises, Y. & Jacquet, S. Bdellovibrio and like organisms: current understanding and knowledge gaps of the smallest cellular hunters of the microbial world. _Crit. Rev.

Microbiol._ 48, 428–449 (2022). Article  PubMed  Google Scholar  * Brown, C. T. et al.Unusual biology across a group comprising more than 15% of domain bacteria. _Nature_ 523, 208–211

(2015). Article  CAS  PubMed  Google Scholar  * Berg, I. A. Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. _Appl. Environ. Microbiol._ 77, 1925–1936

(2011). Article  CAS  PubMed  PubMed Central  Google Scholar  * He, C. et al. Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in

groundwater ecosystems. _Nat. Microbiol._ 6, 354–365 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  * Tian, R. et al. Small and mighty: adaptation of superphylum

Patescibacteria to groundwater environment drives their genome simplicity. _Microbiome_ 8, 51 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Ferrier, S., Manion, G., Elith,

J. & Richardson, K. Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment. _Divers. Distrib._ 13, 252–264

(2007). Article  Google Scholar  * Sunagawa, S. et al. Structure and function of the global ocean microbiome. _Science_ 348, 1261359 (2015). Article  PubMed  Google Scholar  *

Delgado-Baquerizo, M. et al. A global atlas of the dominant bacteria found in soil. _Science_ 359, 320–325 (2018). Article  CAS  PubMed  Google Scholar  * Hahn, M. W., Huemer, A., Pitt, A.

& Hoetzinger, M. Opening a next‐generation black box: ecological trends for hundreds of species‐like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit.

_Mol. Ecol. Resour._ 21, 2471–2485 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  * Azan, S. S. E. & Arnott, S. E. The impact of calcium decline on population growth

rates of crustacean zooplankton in Canadian Shield lakes. _Limnol. Oceanogr._ 63, 602–616 (2018). Article  CAS  Google Scholar  * Weyhenmeyer, G. A. et al. Widespread diminishing

anthropogenic effects on calcium in freshwaters. _Sci. Rep._ 9, 10450 (2019). Article  PubMed  PubMed Central  Google Scholar  * Kaushal, S. S. et al. Freshwater salinization syndrome on a

continental scale. _Proc. Natl Acad. Sci. USA_ 115, E574–E583 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  * McKee, L. S. et al. Polysaccharide degradation by the

Bacteroidetes: mechanisms and nomenclature. _Environ. Microbiol. Rep._ 13, 559–581 (2021). Article  CAS  PubMed  Google Scholar  * He, S. et al. Ecophysiology of freshwater Verrucomicrobia

inferred from metagenome-assembled genomes. _mSphere_ 2, e00277-17 (2017). Article  PubMed  PubMed Central  Google Scholar  * Harding, C. J. et al. A lysozyme with altered substrate

specificity facilitates prey cell exit by the periplasmic predator _Bdellovibrio bacteriovorus_. _Nat. Commun._ 11, 4817 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Berlemont, R. & Martiny, A. C. Glycoside hydrolases across environmental microbial communities. _PLoS Comput. Biol._ 12, e1005300 (2016). Article  PubMed  PubMed Central  Google Scholar

  * Garron, M.-L. & Henrissat, B. The continuing expansion of CAZymes and their families. _Curr. Opin. Chem. Biol._ 53, 82–87 (2019). Article  CAS  PubMed  Google Scholar  * Delgado, A.

& Gómez, J. A. in _Principles of Agronomy for Sustainable Agriculture_ (eds Villalobos, F. J. & Fereres, E.) 15–26 (Springer, 2016). * Marmen, S. et al. The role of land use types

and water chemical properties in structuring the microbiomes of a connected lake system. _Front. Microbiol._ 11, 89 (2020). Article  PubMed  PubMed Central  Google Scholar  * Sperlea, T. et

al. The relationship between land cover and microbial community composition in European lakes. _Sci. Total Environ._ 825, 153732 (2022). Article  CAS  PubMed  Google Scholar  * Phale, P. S.,

Sharma, A. & Gautam, K. in _Pharmaceuticals and Personal Care Products: Waste Management and Treatment Technology_ (eds Prasad, M. N. V. et al.) 259–278 (Butterworth-Heinemann, 2019). *

Foley, J. A. et al. Global consequences of land use. _Science_ 309, 570–574 (2005). Article  CAS  PubMed  Google Scholar  * Kaushal, S. S. et al. Land use and climate variability amplify

carbon, nutrient, and contaminant pulses: a review with management implications. _J. Am. Water Resour. Assoc._ 50, 585–614 (2014). Article  CAS  Google Scholar  * Salcher, M. M., Schaefle,

D., Kaspar, M., Neuenschwander, S. M. & Ghai, R. Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae. _ISME J._ 13,

2764–2777 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  * Biessy, L., Pearman, J. K., Waters, S., Vandergoes, M. J. & Wood, S. A. Metagenomic insights to the functional

potential of sediment microbial communities in freshwater lakes. _Metabarcoding Metagenom._ 6, e79265 (2022). Article  Google Scholar  * Linz, A. M. et al. Freshwater carbon and nutrient

cycles revealed through reconstructed population genomes. _PeerJ_ 6, e6075 (2018). Article  PubMed  PubMed Central  Google Scholar  * Neuenschwander, S. M., Ghai, R., Pernthaler, J. &

Salcher, M. M. Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria. _ISME J._ 12, 185–198 (2018). Article  CAS  PubMed  Google Scholar  * NSERC Canadian Lake

Pulse Network. _NSERC Canadian Lake Pulse Network Field Manual 2017–2018–2019 Surveys_ (eds Varin, M.-P. et al.) https://doi.org/10.17118/11143/18662 (Université de Sherbrooke, 2021). *

Hengl, T. et al. SoilGrids250m: global gridded soil information based on machine learning. _PLoS ONE_ 12, e0169748 (2017). Article  PubMed  PubMed Central  Google Scholar  * Muñoz Sabater,

J. _ERA5-Land Hourly Data from 1981 to Present_ (Copernicus Climate Change Service (C3S) Climate Data Store (CDS), 2019). * _Canadian Environmental Quality Guidelines. Canadian Water Quality

Guidelines for the Protection of Aquatic Life. Phosphorus: Canadian Guidance Framework for the Management of Freshwater Systems_ (Canadian Council of Ministers of the Environment, 2004). *

_Canada Ecozones_ (Canadian Council on Ecological Areas, 2014); https://ccea-ccae.org/ecozones-downloads/ * Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for

Illumina sequence data. _Bioinformatics_ 30, 2114–2120 (2014). Article  CAS  PubMed  PubMed Central  Google Scholar  * Li, D. et al. MEGAHIT v1.0: a fast and scalable metagenome assembler

driven by advanced methodologies and community practices. _Methods_ 102, 3–11 (2016). Article  CAS  PubMed  Google Scholar  * Li, H. & Durbin, R. Fast and accurate short read alignment

with Burrows-Wheeler transform. _Bioinformatics_ 25, 1754–1760 (2009). Article  CAS  PubMed  PubMed Central  Google Scholar  * Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for

robust and efficient genome reconstruction from metagenome assemblies. _PeerJ_ 7, e7359 (2019). Article  PubMed  PubMed Central  Google Scholar  * Parks, D. H., Imelfort, M., Skennerton, C.

T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. _Genome Res._ 25, 1043–1055 (2015). Article

  CAS  PubMed  PubMed Central  Google Scholar  * Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved

genome recovery from metagenomes through de-replication. _ISME J._ 11, 2864–2868 (2017). Article  CAS  PubMed  PubMed Central  Google Scholar  * Seemann, T. Prokka: rapid prokaryotic genome

annotation. _Bioinformatics_ 30, 2068–2069 (2014). Article  CAS  PubMed  Google Scholar  * Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site

identification. _BMC Bioinformatics_ 11, 119 (2010). Article  PubMed  PubMed Central  Google Scholar  * Nawrocki, E. P. & Eddy, S. R. Infernal 1.1: 100-fold faster RNA homology searches.

_Bioinformatics_ 29, 2933–2935 (2013). Article  CAS  PubMed  PubMed Central  Google Scholar  * Kalvari, I. et al. Rfam 14: expanded coverage of metagenomic, viral and microRNA families.

_Nucleic Acids Res._ 49, D192–D200 (2021). Article  CAS  PubMed  Google Scholar  * Aramaki, T. et al.KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold.

_Bioinformatics_ 36, 2251–2252 (2020). Article  CAS  PubMed  Google Scholar  * Saier, M. H. et al. The Transporter Classification Database (TCDB): recent advances. _Nucleic Acids Res._ 44,

D372–D379 (2016). Article  CAS  PubMed  Google Scholar  * Finn, R. D., Clements, J. & Eddy, S. R. HMMER web server: interactive sequence similarity searching. _Nucleic Acids Res._ 39,

W29–W37 (2011). Article  CAS  PubMed  PubMed Central  Google Scholar  * Zhang, H. et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. _Nucleic Acids Res._ 46,

W95–W101 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  * Terrapon, N., Lombard, V., Gilbert, H. J. & Henrissat, B. Automatic prediction of polysaccharide utilization loci

in Bacteroidetes species. _Bioinformatics_ 31, 647–655 (2015). Article  CAS  PubMed  Google Scholar  * Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing

genomic features. _Bioinformatics_ 26, 841–842 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  * Bushnell, B. BBMap (SourceForge, 2015). * Jain, C., Rodriguez-R, L. M.,

Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. _Nat. Commun._ 9, 5114 (2018). Article 

PubMed  PubMed Central  Google Scholar  * Li, H. et al. The Sequence Alignment/Map format and SAMtools. _Bioinformatics_ 25, 2078–2079 (2009). Article  PubMed  PubMed Central  Google Scholar

  * Nayfach, S. & Pollard, K. S. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. _Genome Biol._ 16, 51

(2015). Article  PubMed  PubMed Central  Google Scholar  * Castro, J. C. et al. imGLAD: accurate detection and quantification of target organisms in metagenomes. _PeerJ_ 6, e5882 (2018).

Article  PubMed  PubMed Central  Google Scholar  * Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.

_Bioinformatics_ 36, 1925–1927 (2019). Article  PubMed  PubMed Central  Google Scholar  * Yu, G., Smith, D. K., Zhu, H., Guan, Y. & Lam, T. T. ggtree: an R package for visualization and

annotation of phylogenetic trees with their covariates and other associated data. _Methods Ecol. Evol._ 8, 28–36 (2017). Article  Google Scholar  * Nurk, S., Meleshko, D., Korobeynikov, A.

& Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. _Genome Res._ 27, 824–834 (2017). Article  CAS  PubMed  PubMed Central  Google Scholar  * Huntemann, M. et al. The

standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4). _Stand. Genomic Sci._ 11, 17 (2016). Article  PubMed  PubMed Central  Google Scholar  * Caporaso, J. G.

et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. _Proc. Natl Acad. Sci. USA_ 108, 4516–4522 (2011). Article  CAS  PubMed  Google Scholar  *

Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. _EMBnet J._ 17, 10–12 (2011). Article  Google Scholar  * Callahan, B. J. et al. DADA2: high-resolution

sample inference from Illumina amplicon data. _Nat. Methods_ 13, 581–583 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  * Alishum, A. DADA2 formatted 16S rRNA gene sequences

for both bacteria & archaea. _Zenodo_ https://doi.org/10.5281/zenodo.3951383 (2020). * Oksanen, J. et al. vegan: an R package for community ecologists (CRAN, 2020). * Paradis, E. &

Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. _Bioinformatics_ 35, 526–528 (2019). Article  CAS  PubMed  Google Scholar  * Fitzpatrick, M. C.

et al. gdm: generalized dissimilarity modeling (CRAN, 2021). * R Core Team. _R: A Language and Environment for Statistical Computing_ (R Foundation for Statistical Computing, 2021). *

Wickham, H. et al. Welcome to the tidyverse. _J. Open Source Softw._ 4, 1686 (2019). Article  Google Scholar  * Garner, R. et al. The LakePulse Metagenome-Assembled Genome catalogue. _Dryad_

https://doi.org/10.5061/dryad.zkh1893fs (2023). Download references ACKNOWLEDGEMENTS This study was funded by the NSERC Canadian LakePulse Network (Strategic Network Grant NETGP-479720) and

Canada Research Chairs held by D.A.W. and Y.H. R.E.G. and V.E.O. received scholarships from the NSERC CREATE ÉcoLac Training Program in Lake and Fluvial Ecology. R.E.G. also received

support from a Fonds de recherche du Québec _–_ Nature et technologies Doctoral Research Scholarship and the Stephen Bronfman Graduate Scholarship in Environmental Studies. The pan-Canadian

field campaigns were made possible through the immense commitment and efforts of the LakePulse sampling crews and support teams, and the cooperation and assistance of Indigenous groups,

municipal and park employees, lake associations and landowners. We thank the LakePulse researchers involved in the generation, management and quality control of the dataset, and acknowledge

contributions from J. Juric, P. MacKeigan, C. Paquette, M. Beaulieu, K. Griffiths, G. Potvin, B. Cremella, G. Diab, V. Fugère, J. Kim, A. Oliva and K. Velghe. We also thank W. Brookes, S.

Simpson and Compute Canada for bioinformatics technical support. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Department of Biology, Concordia University, Montreal, Quebec, Canada Rebecca

E. Garner, Vera E. Onana & David A. Walsh * Groupe de recherche interuniversitaire en limnologie, Montreal, Quebec, Canada Rebecca E. Garner, Vera E. Onana, Yannick Huot & David A.

Walsh * Environment and Climate Change Canada, Montreal, Quebec, Canada Susanne A. Kraemer * Département de géomatique appliquée, Université de Sherbrooke, Sherbrooke, Quebec, Canada Maxime

Fradette, Marie-Pierre Varin & Yannick Huot Authors * Rebecca E. Garner View author publications You can also search for this author inPubMed Google Scholar * Susanne A. Kraemer View

author publications You can also search for this author inPubMed Google Scholar * Vera E. Onana View author publications You can also search for this author inPubMed Google Scholar * Maxime

Fradette View author publications You can also search for this author inPubMed Google Scholar * Marie-Pierre Varin View author publications You can also search for this author inPubMed 

Google Scholar * Yannick Huot View author publications You can also search for this author inPubMed Google Scholar * David A. Walsh View author publications You can also search for this

author inPubMed Google Scholar CONTRIBUTIONS D.A.W. conceived the study and designed the analyses with R.E.G. R.E.G., S.A.K. and V.E.O. performed the bioinformatic analyses. M.F. performed

the geomatic analyses. M.-P.V. coordinated the LakePulse field campaigns and data quality control. Y.H. conceived and directed the LakePulse Network. R.E.G. and D.A.W. wrote the manuscript.

All authors read and improved the final manuscript. CORRESPONDING AUTHOR Correspondence to David A. Walsh. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing interests.

PEER REVIEW PEER REVIEW INFORMATION _Nature Microbiology_ thanks Luis Rodriguez-R, Helmut Bürgmann and the other, anonymous, reviewer(s) for their contribution to the peer review of this

work. Peer reviewer reports are available. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional

affiliations. EXTENDED DATA EXTENDED DATA FIG. 1 Project workflow illustrating the generation and analysis of the LakePulse MAG catalogue. EXTENDED DATA FIG. 2 Distributions of (A)

geography, (B) lake morphometry, (C) watershed soil, (D) land use, (E) climate, and (F) surface water physicochemistry variables. Colours represent ecozones and ecozone medians are indicated

by dashed lines. EXTENDED DATA FIG. 3 Number of MAGs generated within each ecozone co-assembly. EXTENDED DATA FIG. 4 Comparison of taxonomic diversity in MAG and 16S rRNA gene ASV datasets:

percentages of MAGs and ASVs assigned to (A) phyla and (B) orders. EXTENDED DATA FIG. 5 Phylum-level biogeographic distributions of MAGs. EXTENDED DATA FIG. 6 HIERARCHICAL CLUSTERING

(WARD’S LINKAGE) OF MAG PHYLUM-LEVEL TAXONOMIC ASSEMBLAGES. Letter symbols above each MAG assemblage (scaled to relative TAD80) represent ecozones and coloured squares represent lake

chlorophyll-_a_ concentration. EXTENDED DATA FIG. 7 PCoAs of (A) the taxonomic variation among ASV assemblages based on Jaccard dissimilarities and (B) the variation in metabolic gene

content among metagenomes based on Bray-Curtis dissimilarities. EXTENDED DATA FIG. 8 SIGNIFICANT PREDICTORS OF (A) TAXONOMIC AND FUNCTIONAL TURNOVER ACROSS MAG ASSEMBLAGES AND COMMUNITY

PROFILES AND (B) TURNOVER IN SPECIFIC METABOLIC FUNCTIONS ACROSS MAG ASSEMBLAGES. The height of bars represents the relative importance of predictors within the GDM. MAG assemblage turnover

is shown above zero and community (ASV or metagenome) turnover is shown below zero. EXTENDED DATA FIG. 9 GENE MAPS OF POLYSACCHARIDE UTILIZATION LOCI (PULS) IDENTIFIED ACROSS _BACTEROIDOTA_

MAGS. Arrows indicate gene directions. Colours represent gene types (SusCD, CAZymes, tRNA genes, other KOs). EXTENDED DATA FIG. 10 PCoA showing the variation in xenobiotics biodegradation

and metabolism among MAG assemblages. SUPPLEMENTARY INFORMATION REPORTING SUMMARY SUPPLEMENTARY TABLES 1–4 Supplementary Table 1: Summary of metagenome information: lake names, accession

information, sampling coordinates and assembly characteristics. Table 2: Summary of MAG quality, characteristics, taxonomy, associated file names, marker gene content and TAD80 across 300

freshwater to oligosaline lakes. Table 3: Number of novel MAGs in each phylum. Table 4: Generalized dissimilarity modelling results for MAG assemblages and community (ASV and metagenome)

profiles across lakes based on taxonomic and functional composition. PEER REVIEW FILE SOURCE DATA SOURCE DATA FIG. 1 Statistical source data. SOURCE DATA FIG. 2 Statistical source data.

SOURCE DATA FIG. 3 Statistical source data. SOURCE DATA FIG. 4 Statistical source data. SOURCE DATA FIG. 5 Statistical source data. RIGHTS AND PERMISSIONS Springer Nature or its licensor

(e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted

manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Garner,

R.E., Kraemer, S.A., Onana, V.E. _et al._ A genome catalogue of lake bacterial diversity and its drivers at continental scale. _Nat Microbiol_ 8, 1920–1934 (2023).

https://doi.org/10.1038/s41564-023-01435-6 Download citation * Received: 01 October 2022 * Accepted: 20 June 2023 * Published: 31 July 2023 * Issue Date: October 2023 * DOI:

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