Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota.

Bacteria / genetics Lakes / microbiology Metagenome Metagenomics Phylogeny

Journal

Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192

Informations de publication

Date de publication:
04 Sep 2024
Historique:
received: 28 12 2023
accepted: 27 08 2024
medline: 5 9 2024
pubmed: 5 9 2024
entrez: 4 9 2024
Statut: epublish

Résumé

The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.

Identifiants

DOI: 10.1038/s41597-024-03826-8 PMID: 39231974
pubmed: 39231974
doi: 10.1038/s41597-024-03826-8
pii: 10.1038/s41597-024-03826-8
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

966

Subventions

Organisme : NSF | BIO | Division of Environmental Biology (DEB)
ID : DEB-2025982
Organisme : NSF | BIO | Division of Environmental Biology (DEB)
ID : DEB-1344254
Organisme : NSF | BIO | Division of Molecular and Cellular Biosciences (MCB)
ID : MCB-0702395
Organisme : United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)
ID : WIS01516, WIS01789, WIS03004
Organisme : NSF | BIO | Division of Biological Infrastructure (DBI)
ID : DBI-2011002
Organisme : U.S. Department of Energy (DOE)
ID : 89233218CNA000001
Organisme : U.S. Department of Energy (DOE)
ID : DE-AC05-76RL01830
Organisme : U.S. Department of Energy (DOE)
ID : DE-AC05-00OR22725
Organisme : U.S. Department of Energy (DOE)
ID : DE-AC02-05CH11231
Organisme : U.S. Department of Energy (DOE)
ID : 17-SC-20-SC

Informations de copyright

© 2024. The Author(s).

Références

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Auteurs

Tiffany Oliver (T)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. toliver4@spelman.edu.
Department of Biology, Spelman College, Atlanta, GA, 30314, USA. toliver4@spelman.edu.

Neha Varghese (N)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Simon Roux (S)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Frederik Schulz (F)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Marcel Huntemann (M)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
ORCID: 0000-0002-1284-3748

Alicia Clum (A)

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Brian Foster (B)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Bryce Foster (B)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Robert Riley (R)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Kurt LaButti (K)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Robert Egan (R)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Patrick Hajek (P)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Supratim Mukherjee (S)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
ORCID: 0000-0002-6322-2271

Galina Ovchinnikova (G)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

T B K Reddy (TBK)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
ORCID: 0000-0002-0871-5567

Sara Calhoun (S)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Richard D Hayes (RD)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
ORCID: 0000-0002-5236-7918

Robin R Rohwer (RR)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA.
ORCID: 0000-0002-2664-6489

Zhichao Zhou (Z)

Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
ORCID: 0000-0002-9120-6762

Chris Daum (C)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
ORCID: 0000-0003-3895-5892

Alex Copeland (A)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
ORCID: 0000-0002-3971-5439

I-Min A Chen (IA)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Natalia N Ivanova (NN)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
ORCID: 0000-0002-5802-9485

Nikos C Kyrpides (NC)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
ORCID: 0000-0002-6131-0462

Nigel J Mouncey (NJ)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Tijana Glavina Del Rio (TG)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Igor V Grigoriev (IV)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.
ORCID: 0000-0002-3136-8903

Steven Hofmeyr (S)

Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Leonid Oliker (L)

Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Katherine Yelick (K)

Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Electrical Engineering and Computer Sciences Department, University of California Berkeley, Berkeley, CA, 94720, USA.

Karthik Anantharaman (K)

Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
ORCID: 0000-0002-9584-2491

Katherine D McMahon (KD)

Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA.

Tanja Woyke (T)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA.
ORCID: 0000-0002-9485-5637

Emiley A Eloe-Fadrosh (EA)

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. eaeloefadrosh@lbl.gov.
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. eaeloefadrosh@lbl.gov.
ORCID: 0000-0002-8162-1276

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Classifications MeSH

questionsmedicales.fr › Bactéries › Coassembly and binning of a twenty-year...
questionsmedicales.fr › Environnement et santé publique › Environnement › Eau douce › Lacs › Coassembly and binning of a twenty-year...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Métagénome › Coassembly and binning of a twenty-year...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Métagénomique › Coassembly and binning of a twenty-year...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Coassembly and binning of a twenty-year...