Scientific Data (Sep 2024)
Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota
- Tiffany Oliver,
- Neha Varghese,
- Simon Roux,
- Frederik Schulz,
- Marcel Huntemann,
- Alicia Clum,
- Brian Foster,
- Bryce Foster,
- Robert Riley,
- Kurt LaButti,
- Robert Egan,
- Patrick Hajek,
- Supratim Mukherjee,
- Galina Ovchinnikova,
- T. B. K. Reddy,
- Sara Calhoun,
- Richard D. Hayes,
- Robin R. Rohwer,
- Zhichao Zhou,
- Chris Daum,
- Alex Copeland,
- I-Min A. Chen,
- Natalia N. Ivanova,
- Nikos C. Kyrpides,
- Nigel J. Mouncey,
- Tijana Glavina del Rio,
- Igor V. Grigoriev,
- Steven Hofmeyr,
- Leonid Oliker,
- Katherine Yelick,
- Karthik Anantharaman,
- Katherine D. McMahon,
- Tanja Woyke,
- Emiley A. Eloe-Fadrosh
Affiliations
- Tiffany Oliver
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Neha Varghese
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Marcel Huntemann
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Alicia Clum
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
- Brian Foster
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Bryce Foster
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Robert Riley
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Kurt LaButti
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Robert Egan
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Patrick Hajek
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Supratim Mukherjee
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Galina Ovchinnikova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- T. B. K. Reddy
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Sara Calhoun
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Richard D. Hayes
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Robin R. Rohwer
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison
- Chris Daum
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Alex Copeland
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- I-Min A. Chen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Natalia N. Ivanova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Nikos C. Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Nigel J. Mouncey
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Tijana Glavina del Rio
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Igor V. Grigoriev
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Steven Hofmeyr
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory
- Leonid Oliker
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory
- Katherine Yelick
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory
- Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison
- Katherine D. McMahon
- Department of Bacteriology, University of Wisconsin-Madison
- Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- Emiley A. Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
- DOI
- https://doi.org/10.1038/s41597-024-03826-8
- Journal volume & issue
-
Vol. 11,
no. 1
pp. 1 – 7
Abstract
Abstract 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.
